Well, in Switzerland, where all my customers are, they never use the dual load configuration approach.
So maybe in your part of the world, this is a popular model, but not here...
I cannot help you with some scripts.
What our customers are doing, are more backups, or some are using database replications, and TSM functionality to ensure high availability. Until now, they are quite happy.
They are not quite interested with the dual load approach, exactly because of this discrepancy problem.
The comparison you're talking about in V9.5 is only something that compares CMOD resources (users, groups, application groups, etc...) but not customer datas.
One last question, when you say 1 side you have 1000 hits, and the other side you have only 997... have you looked a the differences? Is there some missing load? Or are all the load there, but one of them is smaller than what was expected? Or do you have some "hidden" process that load documents into the first CMOD, but not on the second? Where there some operations done in the first or second CMOD that was "manually" done, and didn't got replicated to the other one?