severe vibration after t5 swap

At this point T5 out of car with bellhousing , pp, clutch on car and new motor mounts, still vibrates. Used old flywheel, bh, pp, clutch during orginal install. Getting ready to remove bh, pp, clutch and see if still vibrates. If vibrates, will remove flywheel and test again, if still vibrates, may have to replace crankshaft bearings? Have already replaced harmonic balancer, water pump, alternator.
 
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Back to the drawing board
Is the engine running on 8 cylinders?
Do you have mismatched parts
Does the crank imbalance match the weight balance of the flywheel and damper?
Base engine concern, bent rod etc.
Pull the engine apart
Have the crank balanced with the damper and flywheel/ flex plate / piston rod combo
 
Posts #32, #38, #77 - Just to recap the mechanicals - OP reused the original bell housing, flywheel, clutch, pressure plate, and pilot bearing however the throw out bearing was/is new and used an adaptor plate to install the T5 on the original bell housing. Car had zero vibrations before swap. Is this correct and if not what has changed?

Posts #24, #26, #57, #71, & #75 - OP and/or mechanic(s) removed the transmission but left everything else and the motor ran as smooth as silk. Reinstalled the transmission with only the yolk in the tail shaft and the vibration was present in all gears even with the clutch in. Again, OP please verify this and who removed the transmission and verified there was no vibration.

Post #101 - Now with the transmission removed it vibrates?

Pull it all off and verify that the motor all by itself does not vibrate. Add components back one at a time (flywheel, clutch & pressure plate, etc. until it vibrates. IF it is back to when the transmission it hung then I still come back to an alignment issue.

Who's adapter plate did you use?
 
Post #101 - Now with the transmission removed it vibrates? Yes, apparently my mechanic did not feel the vibration!?? My son and I are now doing the work and are in process of stripping down to flywheel and retesting. I guess will have to reinstall BH and starter to test unless someone knows of another way to start engine? By the way, why is everyone so uptight about reaching top 2 bolts on BH? I can see them from under hood and can easily reach them with wrench from the top!
 
Posts #32, #38, #77 - Just to recap the mechanicals - OP reused the original bell housing, flywheel, clutch, pressure plate, and pilot bearing however the throw out bearing was/is new and used an adaptor plate to install the T5 on the original bell housing. Car had zero vibrations before swap. Is this correct and if not what has changed? All is true, used :

California Pony Cars T-5 Adapter Plate Mustang With 6-Bolt Bellhousing 1965-1973​

California Pony Cars:
TRA 650 526
 
Did you make sure that the part number on your bell housing was one of the ones that this adapter works with?

- C5AA-6394-A -C5AA-6394-B -DSA-6394-AB
- C5DA-6394-A -C5TA-6394-A
- C9OA-6394-A -D1TA-6394-AA
- D2OA-6394-AA -D1TA-6384-A

I have attached the installation instructions (pictures would have been a huge bonus) and there is potential for misalignments so again I come back to checking the alignment of the T5 to the centerline of the crank. You also need to check the endplay on the input shaft of the T5 as it is just good practice.
 

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