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Before they resurfaced the flywheel they told me that the old wear was flush on one side but had a lip on the other, they said there were also a few heat marks on it and that when they ran it on the machine that they run somthing right up to the flywheel and if the flywheel moves back in forth from it then they said its warped...Of course after saying that Im kinda wondering if its possible that it just had uneven wear or somthing. They said one side looks almost .25 deeper than the other, I had the whole thing cut to that level then and got the shim for it. When I got it back they said that they had trouble with the heat marks but had cut the whole thing down and I guess "fixed" the warp that way.
As far as the weights I started the numbers on the first one, there were weights on 1,2, and a small one on 3 (going clockwise), then no weights at all on the rest.
I assumed you used a machine to balance everything and it couldnt be done accurately in car, if it can that would be amazing. lol
The best balance is dynamic in the vehicle. Yes, I use a high dollar analyzer and two triaxle accelerometers for my balance jobs. On average they take about two hours to zero in on the final fix.
Where was the shim used and how thick is it?
I would have put in a new flywheel in place of having the old one resurfaced. If your plan is to replace it, just have the NEW flywheel and pressure plate balanced together. Make sure to index them so you install in the same orientation as when balanced.