Yeah, that would do it. Years ago I read about someone who added extra washers under the bolts for some reason. I had forgotten about that. It was in one of those "Say Smokey?" columns I think.

Did you use new bolts? If so, is there any chance they have taller heads than the original ones?

Does the whining go away with the transmission in neutral and pedal up?

I guess it has to come apart anyway. If the bolts are standing to high, you'll see the marks.