Good advice. My last conversation with Paul after I took my car back in was less than friendly.
So, I dropped in today with a dozen donuts for Paul and found him fabricating a stand to run the engine on outside of the car. He had the engine out and hanging above the stand that he was making. The clutch was off of the flywheel. I asked, "Have you sent the flywheel and clutch to check for balance?" "No." "Why not?" "I'd have to remove the oil pan to get the flywheel off to do that. I decided to run the engine without the clutch and see how it goes." That is exactly what Fort Wayne Clutch said to do when I called them and told them my mechanic thinks the clutch is out of balance. But, it would seem easier to me to check the flywheel and clutch on a balancer before building a stand and running the engine. Oh well. Each to his own.
Just opinion here, and we all know what that is worth....
At this point, or at this juncture, I don't see much point in trying to run the engine. You have already run it. The 'stand' was your car. You already know it vibrates. All your mechanic can do, is run it with and without the PP & disc. After that, if the flywheel is removed, I think Paul does not have a way to start it. Not much point in building a stand, for so little return.
In my area, I have a clutch place (called Clutch Masters), that can (and does) run the flywheel, with & without the PP. It's so quick and easy, they don't even charge to do it. (And, if they do a balance, drill hole(s), the charge is very minimal.) So, if a problem is found with the clutch and flywheel, then it needs to be corrected. I assume you & Paul have access to such a place in your local area.
At that point, then the engine, with flywheel & clutch, need to be run. And, if it still vibrates, well... you know what's next.
It would be nice if you have access to a vibration meter. It would remove guess work from 'how much vibration is acceptable'. If Paul runs it now, I would imagine he would run it with the PP installed (baseline), then run again with PP removed. If there is a problem, he would hopefully feel the difference. With a meter, he could know for sure if there is a problem. The meter that I'm thinking of, and the one I have used, has a probe that you hold against suspect areas - in this case, near the rear main, probably where the pan bolts to the block.
As said... Just opinion
BTW, if you had/have a meter, you can also hold the probe near the center main (on the pan rail), and near the front main. Usually, this will direct you to the area where vibration is coming from. For example, pistons/rods/crank, near the front, or near the middle main. This is usually good for rotating machinery, motors, driveshafts, and the like. Not sure if this would work on a running engine.