He's not going to warp an aluminum flywheel from bolting it down wrong. I had an aluminum flywheel for 100k miles, on nitrous, no problems. I know plenty of people who have had no problems. Your comment about losing bottom end and going too light isn't true, as I ran a 7lb and wouldn't have traded it for the world.

As for this problem....you're going to have to take the tranny off again and make sure everything is correct. Make sure everything seats and bolts up properly...if you can't get it, tow it to a shop so they can get it right.