NotchRocket - there's no such thing as two "identical" engines. When you start measuring at blueprint-level dimensions, you'll find all sorts of differences that result in slightly different compression ratios, different cylinder sealing, slightly different bores and strokes which results in different displacements, etc. What kind/weight oil were they running and what was the oil temp? That can make a difference. Even "identical" cams are rarely identical. And even if the cams were close to the same, were they installed with the same timing? There are many other factors that impact the dyno runs - driveline differences (the tranny differences you mentioned can make a diffrence), what kind of shape the limited slips are in, type/age of fluid in tranny's and rearends, drive shaft type, shape of the ujoints, tire type, size and air pressure, how they were strapped down (I've seen one extra click on the tie down straps show an change of 10 rwhp on the same car - no other changes) -- the list goes on and on. The best you can conclude based on what you've stated thus far is that the cars make about the same power.
One last thing - you have to be really careful about what's concluded from dyno runs. I recently spectated at a local dyno day. The operator got almost all the way through 3 runs before realizing that there was a malfunction with the dyno brake that was throwing all the runs off on the low side. The cars had to be retested. The tough part was one guy had done some tuning via computer based on what turned out to be invalid data.
Chassis dynos are alot like a good fictional novel. VERY entertaining; but you need a reality check after you get through with them. They're somewhat useful for tuning on the same car during the same strapdown session - although if you're looking for incremental gains of less than 10HP, you're kidding yourself. They're not that repeatable. Comparing two different cars on the same day, same dyno, same operator may give you a rough idea of the differences. Comparing two different cars by looking at dyno numbers off of different dynos, at different locations, under different conditions with different operators is complete fiction.