I will assume they left the 428 externally balanced and you did use a 428 flywheel both times on the dyno. I'd see if you can get the balance card from the original shop that did the balance work and check the bob weight against another typical bob weight on another 428....this is the first step I'd take to be sure they did the math correct or at least find out if it's in the ball park...I'm sure we can find the correct weights for what ever combination you have....let's get that verified first......
The record should look something like this one...
http://www.gessford.com/images/balancecardcj.gif
if this is in the ball park then see if they balanced it with the clutch plate and if that's indexed for any reason because it wasn't perfectly neutral.....and running without it in this special case is causing a problem.
George