OK, 2 motors identical, same everything will not run the same....as far as timing is concerned, alot of motors like to run at 35+ degrees....as you back down toward TDC the motor will start laboring hard. Timing sets have diff. keys, diff springs in distrib's, alot of things can happen to get your timing off. Take your time, set everything to the exact point....you should be fine.
On a blower motor, fluffy mixture is good....best too rich than too lean. Don't call in the Marines until the bad crap starts to fly!
We build alot of motors for race folk, and each one we index everything so everything is the same. Then, run them on the dyno. Each and every motor, though totally identical does produce within 50 horses of each other. Your talking about 4500horses, 50 is something you can't feel at the accelerator. Every motor, even after we dyno it, and makes with a few horses of one another, each one pulls differently....more power here, more power there....
Verify TDC, check everything, leave nothing to chance, same springs, same distrib. weights, same shimmed distributor end clearances. If your running a button in your timing gear cover, this will also change your overall timing. If your running a vacuum advance, does it have the adjustable can? Or is the system electronically advanced? IS the cam degreed in?
As you can see, getting to where you were with a new motor, even though the same motor, can be a chore. Motor vaccum also plays a part in this, as well as vacuum leaks....
Its a hotrod, once you get everything as you want it, things should not move again until a piece of the puzzle is changed.
On a blower motor, make sure you are rich mixture wise, all the time....if you don't you'll torch your pistons. Also, run your motor a little on the warm side, with a piece of cardboard over the outside of the radiator, with holes cut in it to restrict airflow....that way you can get your rings to seal.... run the motor for 3 or 4 hours like that....get her to about 220-210, very your rpm slightly, rev every once in a while....