issues after a trans swap...

alright, i know that you have to drive the car a while before it will run "properly" again, but im having a few issues that dont seem to be related the ecm having to relearn it perameters....

alright, she had been with out power to the ecm for a week, so obviously she has to relearn everything... but, shes not running NEARLY as strong as she used to :disappoin ... and, she sounds like the timings fairly off on her... would the computer adjust this as it relearns while driving, or do i have to do what i think i ahve to do and go through and adjust the timing manually...

also, she doesnt have the low end punch that she used to have... is this just the fact that shes still learning how to drive and that shes a little outta time? or, is the gearing different in the 4t60s? the one i got is outta a 92 cutlass supreme and mines a 94 z34... i do believe that there were different final drive gearings, but, i may be wrong.... also, in overdrive(when she finally downshifts to overdrive) shakes... i think its tied in with the engine not quite running properly right but, i dont know...

thanx for you help!