200K+ miles. Manual transmission is really difficult when shifting. Can’t get into reverse until warmed up. Have New slave cylinder and hydraulic lines. Had trans fluid changed, as well. Not sure if synthetic fluid is the culprit? Problem goes away after driving a bit.
Does the transmission shift easily without the engine running?
Tester
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You replaced the slave cylinder what about the clutch master cylinder? Have you replaced it or at least had it checked?
If you can shift between the gears when the engine isn’t running this would suggest that the clutch isn’t quite fully disengaging - this can wear the synchros when shifting and overheat the clutch and flywheel if you’re in the habit of keeping it in gear with the clutch down when stopped, which is tempting when one has this problem. This happened to me with a van of about the same mileage as your car and may have been due to wear of pressure plate components, but before going there you’ll want to recheck the full linkage path, cylinders, etc.
If you’re in a pinch and must drive it (like to the repair shop), consider putting the car in first or reverse before starting the engine, slipping it out of gear just before a full stop and, when fully stopped, killing the engine before shifting back into gear - this will allow you to drive some while avoiding damage from partial clutch engagement when idling. If you must leave it for someone else to drive (like at a repair shop), leave a note explaining this taped to the steering wheel where they can’t miss it. Don’t coast with the engine off, steering locked, etc.
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Heya everyone, thank you all for the replies! I’m in a pandemic/economic pinch - in that I have to keep this car running for now.
The master cylinder is in good shape - probably less than 50K miles on it (car has 200K+)
Just replaced the slave and lines - they were leaking.
I can shift easily when the car engine is not running.
As soon as I start from cold - there is no going into reverse or first without forcing it (which is clearly not a good idea but I had to do what I had to do to get it back into the driveway).
Also - when the car is still warming up / shifting roughly, I notice as I shift (depress clutch pedal, still in gear) the car feels like it’s slowing down, like there’s no neutral.
Again, all these issues go away after driving 10-15 minutes.
edit: I did some digging into my service records - so this is a little embarrassing.
Clutch (disc, etc) was last done about 120K miles ago. 
Sounds like the clutch master cylinder is leaking internally.
Tester
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It sounds like your clutch is not fully disengaging, there could be several reasons as suggested in the responses. If you value your transmission don’t ever force it into a gear while the engine is running. To start from stopped, put it into gear with the engine off, then start engine and let out the clutch. After a full stop, kill the engine before shifting into gear and restarting just before you need to roll. If you know how to double clutch you can help things out when shifting between other gears while rolling - this brings the engine and gears to the same speed, saving the synchros.
To double clutch, slip the transmission into neutral, lift the clutch pedal, set the engine speed to match what will be needed for the next gear (approximately is sufficient for this job), push the clutch back in, shift gears and let out the clutch per usual. Take your time to think it through, but with practice it becomes a habit and takes just seconds, it’s what people did before synchros.
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A bit confused - the car has no trans fluid and where did the synthetic fluid go? In the transmission? The hydraulic clutch system?
This car doesn’t used any synthetic fluid anywhere.
I think you’re right, it’s as if the clutch isn’t fully disengaging. The current clutch system was installed ~2007, ~120K miles ago. From what I can understand the pressure plate is probably “stick a fork in it” d-o-n-e 
The part that I don’t understand (Mechanically) is that I can shift just fine with the engine off. The shifting trouble is only present when the engine is running, and kinda goes away after warming up 15-20mins. I say ‘kinda’ because it’s still rough shifting, but I don’t have to force anything. (fwiw, I only had to force it a couple of times - I now put it into gear and then start the car).
I’m taking it to the shop tomorrow (Thursday) - just down the street. Hopefully I’ll have more info after that.
With the car standing still, engine running, transmission out of gear, and the clutch pushed in but still partially engaged it is turning the input shaft of the transmission (which it wouldn’t do if fully disengaged), so when shifting from neutral into a gear you’re now forcing mechanism that is turning (the input side of the transmission) against mechanism that is standing still (the part of the transmission connected to the wheels) - this is a good way to turn transmission components into metal filings, and maybe big chunks. When the car is stopped with the engine on and transmission in gear with the clutch pedal pushed in but not fully disengaged (such as waiting for a stop light, or train) it will be rubbing on the stationary flywheel, causing wear, heat, and as things progress possibly burning the clutch, maybe glazing or warping the flywheel (as with severely overheated brakes).
The transmission has synchronizing mechanisms, think of them as internal clutches, that bring the transmission input and output components to the same speed when you’re shifting while underway, avoiding grinding. With the clutch not fully disengaged, the synchronizers are stressed substantially harder (more wear) and though they may make it seem like it’s shifting okay they can only mask the problem for a while - they’re being forced to fight the input shaft that is being driven by the not fully disengaged clutch and will wear out faster - in addition to loading your transmission’s gear oil with expensive and abrasive metal filings, after the synchros are worn out and no longer working you’ll be forced to double clutch to avoid grinding on every shift, even after the clutch is fixed.
Continuing to drive this way will cost more $$ in the end (transmissions are considerably more expensive than clutch components). For now you can minimize the damage by always stopping the engine while putting the transmission in gear when stopped, and by double clutching while underway, even when it seems to be shifting okay, or sort of okay (but at the expense of the synchros). If that’s too challenging, then when shifting while the car is moving and with the clutch pedal down, pause a moment while between gears to adjust the engine speed with the accelerator to match what it will be in the next gear. However, unless you plan to dump the car soon you’d be wise to fix it asap. And change your transmission oil to purge those metal filings after things are fixed.
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Subaru manual transmissions typically use 75w90 gear oil. Dinosaur derived and synthetic are both available but according to Subaru forums they don’t like synthetic oil.
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This sounds like the classic symptoms of a clutch that will not fully disengage. The classic reason is that the system needs to be bled. Since you have replaced such a large part of the hydraulic system, bleeding can be a little difficult. Did you re-route the hydraulic lines in a way that leaves a high point for an air bubble? Does multiple rapid pumps of the pedal allow the car to go into gear? Did you accidentally introduce an air bubble while bleeding, by letting the reservoir get low? Concentrate on the hydraulic system, not the transmission.
Faulty clutch master cylinder or air in clutch hydralics my guess. Does pumping pedal prior 2 shifting help? If so mc is prime suspect. It fails but no visible leaks is most common failure mode.
I used to have a couple of Subarus with a stick-shift, and indeed they are picky on gear oils, but it is more complicated than synthetic or not.
The best is to check on Subaru specific forums, but from my recollection the Valvoline synthetic was one of oil brands/types recommended there and it was readily available in local stores, it made trick for me.
I used some another oil before which was OK by spec, but it was harder to get dears engaged with it, so I went with Vlavoline and it was better after that.
The oil would definitely not fix the worn clutch, but with other things in order, it can make a noticeable difference.
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Thanks for the replies!
I don’t see any improvement after pumping the clutch, but will take a closer look at the MC. The reservoir is full.
The new SC and lines were done professionally by the garage I’m about to go back to.
Again (just for posterity) I have absolutley no difficulty shifting when the engine is off.
The problem is intermittent - it goes away after warming up.
If the problem were air in the lines (or other MC leak) wouldn’t the problem persist with the engine off?
No.
With engine off, nothing is rotating.
With the engine running, and if the master cylinder doesn’t allow the full disengagement of the clutch, the gears in the transmission are rotating, which makes the gears grind when trying to shift.
Tester
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Sorry, I didn’t mean to imply the oil was the fundamental problem. I was only answering @Lee_T 's question about synthetic gear oil, what the OP called “transmission fluid.” Having experienced what the OP is going through (in my case with an old Corolla), I’m certain the clutch isn’t disengaging.
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I’m also under impression this is what happening, but he has quite strange thing about symptoms disappearing once car warms up.
That may have something to do with gear oil viscosity, at least potentially.
I did not drive stickshift for 10+ years, and now I do not recall if “hard to engage” symptoms I had on my Subies were anyhow correlating to the car warmed up or not… it was definitely worse on winter, but I recall that replacing gear oil to the one recommended on forums helped across entire range.
No, the problem would NOT persist with the engine off. Any manual tranny will let you shift without even using the clutch if the engine is off. (Occasionally, it might be slightly difficult in a particular gear because gear teeth are tooth-to-tooth…not meshing. But otherwise, you can shift freely.) If your system is not fully bled, it is just like you are not getting the clutch fully pushed down. Any manual car will show difficulty if the clutch is not fully pressed.
The warm engine might allow some expansion to slightly alleviate the problem, but my guess is that even then, as you let the clutch out very slowly, you will find the engagement point is too near the floor. You might even feel some drag even if the clutch is floored…tending to move the car forward.
Take it back to the shop before you damage the first gear synchronizer in the tranny.
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Yes! What you described is spot ont. When the system is cold, the engagement of the clutch is absolutely right at the floor - and it drags even when it’s floored.
It’s in the shop atm. hopeing to hear back by the end of the day. Fwiw, it’s a good shop - I’ve been going to them for 16 years and they’ve always been honest and communicative.