2006 Mustang GT Manual Wont Shift When Warmed Up

Try pumping the clutch pedal when the transmission wont shift to see if that helps. If it does, then the issue could be bleeding, but I think @Tester is correct and this won’t help.

Pumping the clutch helps as it gets more difficult to shift, then ultimately doesn’t help at all once the car is fully warmed up.

What does the clutch pedal feel like as the car warms up? Does it start going to the floor more easily? As it warms up, does the clutch pedal free play increase? Does the clutch engagement point change, getting closer to the floor? Does it make any unusual noises like a howling, grinding, or squeaking sound?

Check your transmission to engine mating, there should be no gap at any point.

If cooling the clutch MC helps, then that part (even if it is newly installed) is most likely defective and should be replaced. I’ve had clutch MC’s fail a couple of times over the years, and they do tend to exhibit the symptoms more after driving a while, they work fine at first but later it is difficult to shift without pumping the clutch pedal. I don’t know if this is b/c of the increased engine compartment temperature or repeated clutch presses when driving distorts the seals even further. Eventually if you don’t do anything about it they won’t work at all of course.

Here’s what you must understand.

If there’s a transition where the clutch pedal works and then doesn’t, you’re probably burning up that new clutch.

Tester

Oh yeah. I’m not driving around like this every day or at all for that matter- this is my third car. I keep it around for fun.

Trying to see if there is anything I can do first. If not, I’d be able to approach my mechanic with the best possible description of the problem and to understand if their proposed fix makes sense.

What I know now is that heat is causing there to be less clutch travel. I’m going to try your water test first. If that doesn’t work, I may replace the hydraulic line between clutch and slave. If that doesn’t work, I’m thinking I got a faulty install or a faulty part in the last clutch kit (less than 5,000 miles ago) and a trip to the mechanic is on order.

I repeat, check your transmission to engine mating. There should be no gap between them all the way around.

That sounds exactly like what I did. I followed Ford’s guidance to a T. Vacuum is def a better term. No bleeder valve on this model.

I’m probably going to need my mechanic to check the mating. Other than heaven duty ramps, my ability to get under this vehicle is rather limited.

Start from the top. You have to lean way over and look at the seam at the back of the engine where it meets and mates to the transmission. Usually this is where the issue is because when the transmission is being installed, the mechanic is looking at the bottom. He would immediately notice any mismatch down there.

Follow that seam from the top down both sides as far as you can see. You have to contort your body some to see most of the seam.

Clutch feel remains the same. Engagement gets lower and lower. One thing to note- the car shifts easier with rapedly depressing clutch. I’m thinking the slave is leaking internally. Would explain a lot.

Slave cylinders don’t leak internally.

They leak externally. And there would be hydraulic fluid on the ground.

Tester

Bummer. There goes that theory. No fluid on ground.

From the manual.
“During each shift, the clutch pedal must be fully depressed to the floor”

Perhaps your linkage gets a little off when warm, adjustment, trans mount, engine mount, sensor, car mat?

Hydraulic clutch!

Tester

Hopefully OP will report back what happens when following Tester’s experiment to try cooling the master cylinder. If that has an effect on the clutch performance, replacing the MC with a new one would be where I’d start. I’d take a look at the linkage between the clutch pedal and MC first of course, just to make sure nothing’s loose down there, or the pedal return spring (if used on this vehicle) has come loose.

I replaced the clutch mc less than 100 miles ago because of these symptoms. Part of me hopes that’s the problem because the part is under warranty. The other part of me really doesn’t want to remove the entire pedal assembly. That sucks. Lol. Just got back from work. Going to check the engine to trans mating, then let it warm up in my driveway and do Testers test (for lack of a better term). I should be back in an hour or so (may try to mow the front lawn too).

It was pretty easy to see the mating from the engine bay. The transmission is mated securely to the engine.

Car is warming up now. Giving Tester’s theory a try.

A visual inspection would be all that’s normally required.

Ok. Warmed up car, ran cool water from the hose over the clutch MC for a few minutes. Still won’t shift.