I had a new clutch put in my '94 civic a few months back during the engine rebuild. I’m anal about saving gas so I tend to shift a bit early, not enough to make the engine chug, but I might shift into 3rd gear at 17 mph. Never had a problem with it. Since the rebuild, when I do shift earlier, the car has hiccups where there is little or no power for a half to full second. The engine will sputter for a bit until I get up into normal operating range. But it’s not like before, I’m shifting no earlier than I have been for the last 6 years and have never dealt with this before. The rpm’s don’t shoot up so I don’t think it’s actually slippage. Any ideas?
That does not sound like a clutch problem, it’s more like an engine problem. I would suggest that you, or the engine rebuilder take a look at the valve lash again, and very soon.
If you have the VTEC engine (EX model), there could be an issue with that system.
Thanks.
How many miles since the rebuild?
I hope you weren’t short-shifting during the early part of break-in.
Likely the new rings are not fully seated in and compression isn’t up to snuff.
If this just started with the new clutch, it’s entirely possible your new clutch does not have the slip necessary to accommodate your short shifting, so it is stressing the engine more than the old clutch did during this early shifting. Try shifting just a little bit later, maybe 200-300 rpm or 2 mph later. If the problem goes away, it was your driving habits. It sounds to me like you are just shifting early enough to lug the engine slightly, which you should probably not do. It’s not good for your engine, and you know how much one of those costs, and it’s probably more than an extra cup or so of gas you will use per tankful shifting just a little bit later.
Going to 3rd gear at 17 mph is mega short shifting. That would put the engine rpms under 1,000 and no wonder it bucks on you. Your short shifting is not saving any gas and is harmful. The new clutch is tighter and is transmitting the motor bucking more noticeably than the old worn out clutch.
You might get away with a shift to 3rd at 17 mph if you are on a downhill grade, but on level ground that is just too soon to be in 3rd gear on a small 4 cylinder motor in your civic. Ideally you should get above 2,000 rpm at least before going to the next gear. If you are on an uphill you need to get to 3,000 and higher before shifting.
Short shifting might keep rpm’s down, put you have to push down on the gas petal more which negates some of the savings from the low rpm. When you need power you need to keep the rpm’s between 3,000 and 6,000. Any rpm’s below 1,500 is in danger of lugging the motor and is not good for the car.
It’s been a good 7,000 miles at least since the rebuild. I’m extremely ashamed to say that I forgot about the break-in for the first 100 miles or so. I didn’t short-shift much, at least not enough to make it lug, or do anything too rough. The notable exception is my 70-80 mph freeway driving I did the first week. Not passing blame here, but I really wish the mechanic would have reminded me. (He’s another story entirely.)
I guess this is more a case of operator incompetence than a mechanical issue. I’ll just stop shifting early.
Thanks everyone.
I would get the compression tested. Low speed stumble is one symptom of low compression.
Modern new engines from the factory don’t need a lot of care breaking in because the tolerances are tight and the finish on the cylinders is carefully controlled.
This is not the case with an engine rebuilt in a small shop.
Did the mechanic drive a few miles before handing it over to you?
Was the cam replaced?
Did you change the oil after 500 miles?
There are some specific things that should have been done in the first few minutes/miles.
When I had a car that was stick shift…I always watched the rpm.
I would make sure the engine compression is good. There’s a dozen ways to rebuild an engine and only one of them is the proper one.
This is an area in which it’s very, very easy for something to go wrong even with care involved.
My bad; the mind was out to lunch. 
A few other possibilities could be a timing belt installed a tooth or two off or improper ignition timing. (Too much retard.)
The ignition timing should be inspected and adjusted with the test plug in use. Failure to do so will throw the timing off quite a bit and this can easily cause a stutter.
I made the mistake of going to a mechanic who did the rebuild really cheap. He has been working on cars since he was a kid, but if he’s been doing it wrong the whole time…
After having dealt with the case of the mysteriously unfindable freon leak over the course of months and 3 shop visits I wouldn’t be surprised if those idiots left rags in all the cylinders. I did change the oil after 500 miles, maybe even sooner. I don’t think the cam was replaced, and when I later asked, it sounded like they didn’t do any sort of bench break in. So I’m saving up for the next rebuild now. If you need a good mechanic in Utah, don’t ask me for any recommendations.