Vibration after new clutch

I've been working and chasing this vibration on my 1995 5.0 for longer than I want to admit. The issue that originally started this was just a noisy throwout bearing, so rationally I bought an all new Ford performance flywheel, throwout bearing, and pilot bearing. A mcloud street pro clutch and pressure plate kit and mcloud clutch fork. Adjustable clutch cable too, and even a short throw shifter to give me something to look forward to. I installed it all myself on jack stands. it all went smoothly, alignment pins stayed in and everything went back together without any force or curse words. I torque specd everything correctly to my knowledge. When I finally start the car, there's a very noticeable vibration through the whole car. Clutch in, vibration. Clutch out in neutral, vibration. In gear clutch out, vibration. I assumed i had not torqued the flywheel or pressure plate correctly so I took off the transmission again and ran the car with only the pressure plate clutch flywheel assembly attached, and it did not vibrate at all. That's when I looked at the mcloud clutch fork and throwout bearing and noticed the mcloud fork does not let the throwout bearing pivot properly, and it was keeping the bearing at an angle, not flat. I also noticed the mcloud pressure plate fingers are shorter than the stock clutch. So the clutch fork was coming in at a further angle to reach the new pressure plate. And since the fork wouldn't even let the bearing pivot, the bearing was at crazy angle.. I assumed this was my problem. So I fixed it by ordering an adjustable pivot stud and also a new Ford performance clutch fork. I was able to extend the pivot stud and fix the geometry of the fork. Believing I fixed my issue I put everything back together and what do you know, vibration is still here. I've been trying to test and think of what this could be before taking everything apart again. I backed off the clutch fork and bearing while it was running to be sure, and since the vibration kept going I know it's not my fork causing it. I heard it could be a problem with my pilot bearing, but I've already tested the car where I start it and just never let the clutch out, and it still vibrates. So I would think that would isolate my problem to just the pressure plate and flywheel assembly. But again, I tested it with the trans completely off and there was no vibration. I've read through so many forums at this point and nothing's making sense for me. Thanks for reading all this and id appreciate any ideas someone has.
 
Welcome to :SN: !

So the problem wasn't present before the swap, or was it? And your checks were done with or without the driveshaft to eliminate driveshaft issues? My first instinct is something to do with the input shaft of the transmission. Whether that's the pilot bushing, a bad bearing, or the input shaft is somehow bent or misaligned, your description leads me there.

Other than that, what is the age of the transmission - all original or has it been rebuilt? Assuming it has the correct input shaft and is engaging the pilot bearing, maybe it also needs some attention.

I'm sure someone will be along to offer their advice as well.
 
Welcome to :SN: !

So the problem wasn't present before the swap, or was it? And your checks were done with or without the driveshaft to eliminate driveshaft issues? My first instinct is something to do with the input shaft of the transmission. Whether that's the pilot bushing, a bad bearing, or the input shaft is somehow bent or misaligned, your description leads me there.

Other than that, what is the age of the transmission - all original or has it been rebuilt? Assuming it has the correct input shaft and is engaging the pilot bearing, maybe it also needs some attention.

I'm sure someone will be along to offer their advice as well.
It was not vibrating before attempting this job. It's the original transmission with the car, 114,000 miles. Holding the clutch in and in first gear, shouldn't that completely stop the transmission from spinning? When I do that the vibration stays the same. Wouldn't this clear any possibility of the transmission or pilot shaft being the problem?
 
The more I think about what you're saying the more I think it's some sort of alignment issue with the input shaft.

Were all of the mating surfaces cleaned as best you could before reinstalling everything? When you installed the transmission, did it seat cleanly before bolting it in or did you need to drive the bolts to seat it? People who brought up the pilot bushing were probably right - if it's worn it'll cause some alignment issues which in turn will cause vibrations.
 
Just food for thought but the next time you have the transmission out of the car check the input shaft end play. Acceptable range for used bearing is 0.002” to 0.005”. My TKO always had a vibration and it took years to figure out it was the end play. Not saying this is it but with the miles you have on that T5 it probably will need some shims.
 
The more I think about what you're saying the more I think it's some sort of alignment issue with the input shaft.

Were all of the mating surfaces cleaned as best you could before reinstalling everything? When you installed the transmission, did it seat cleanly before bolting it in or did you need to drive the bolts to seat it? People who brought up the pilot bushing were probably right - if it's worn it'll cause some alignment issues which in turn will cause vibrations
 
All the mating surfaces were cleaned very flat and the trans went in easily without even guiding it with the bolts. My pilot bearing is new, but the old was chewed up pretty bad and actually fell out when I took off the old clutch. Didn't have to pull it. It scarred up the hole where the pilot bearing goes into a bit, but the new one hammered in straight and tight so I think that's fine. My pilot shaft has a bit of side to side play. How could my transmission be the problem if the vibration occurs even with clutch in and input shaft not spinning? The vibration does not change if clutch is in or out, or if it's in gear or not. And when I have the trans off it doesn't vibrate at all. I feel like my symptoms are enough to clearly know what it is but I just can't figure it out.
 
Check your receipts for the flywheel part number and verify how it's weighted. The vibration sounds like it's completely RPM dependent, personally I wouldn't put too much clout into the fact that it appears to go away with the trans disconnected.

Remove and double check the flywheel.
 
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My pilot bearing is new, but the old was chewed up pretty bad and actually fell out when I took off the old clutch. Didn't have to pull it. It scarred up the hole where the pilot bearing goes into a bit, but the new one hammered in straight and tight so I think that's fine. My pilot shaft has a bit of side to side play.

I feel that this is the most likely culprit.
 
I had a very similar issue in the past that turned out to be an improperly balanced flywheel. (I had ordered the correct one but the manufacturer made some kind of mistake.) Had a bad vibration that was RPM dependent and wouldn't go away with clutch or shifter inputs.

I would be pretty confident in saying that this is your issue except for the fact that you said the vibration went away with just the flywheel and pressure plate installed. Can you go into more detail about how you set up that test?
 
I've been working and chasing this vibration on my 1995 5.0 for longer than I want to admit. The issue that originally started this was just a noisy throwout bearing, so rationally I bought an all new Ford performance flywheel, throwout bearing, and pilot bearing. A mcloud street pro clutch and pressure plate kit and mcloud clutch fork. Adjustable clutch cable too, and even a short throw shifter to give me something to look forward to. I installed it all myself on jack stands. it all went smoothly, alignment pins stayed in and everything went back together without any force or curse words. I torque specd everything correctly to my knowledge. When I finally start the car, there's a very noticeable vibration through the whole car. Clutch in, vibration. Clutch out in neutral, vibration. In gear clutch out, vibration. I assumed i had not torqued the flywheel or pressure plate correctly so I took off the transmission again and ran the car with only the pressure plate clutch flywheel assembly attached, and it did not vibrate at all. That's when I looked at the mcloud clutch fork and throwout bearing and noticed the mcloud fork does not let the throwout bearing pivot properly, and it was keeping the bearing at an angle, not flat. I also noticed the mcloud pressure plate fingers are shorter than the stock clutch. So the clutch fork was coming in at a further angle to reach the new pressure plate. And since the fork wouldn't even let the bearing pivot, the bearing was at crazy angle.. I assumed this was my problem. So I fixed it by ordering an adjustable pivot stud and also a new Ford performance clutch fork. I was able to extend the pivot stud and fix the geometry of the fork. Believing I fixed my issue I put everything back together and what do you know, vibration is still here. I've been trying to test and think of what this could be before taking everything apart again. I backed off the clutch fork and bearing while it was running to be sure, and since the vibration kept going I know it's not my fork causing it. I heard it could be a problem with my pilot bearing, but I've already tested the car where I start it and just never let the clutch out, and it still vibrates. So I would think that would isolate my problem to just the pressure plate and flywheel assembly. But again, I tested it with the trans completely off and there was no vibration. I've read through so many forums at this point and nothing's making sense for me. Thanks for reading all this and id appreciate any ideas someone has.

If you have a roller bearing style pilot bearing that could be your issue as on my car the transmission snout wasnt totally lined up and i actually pushed the center right out of the pilot bearing and that gave me a pretty wicked vibration....