thoughts:
-Most engines seem to like the short yellow VS spring in a dual 600
-I rarely exceed 66 or 67 in primary jet in a 600cfm carb, I'd leave finding the lean limit in jetting until all the other issues are worked out.
-If you aren't totally redoing a carb and just changing jets, I don't see the need for an O2, seems lotsa folks chase their tails, paying more attention to a gauge than to how the engine is running. Pull some plugs, make some guesses.
X2 on the O2. Reference - with the dual Ed 600s that I run on the 302, the A/F from the Innovate interface was good, 13ish mostly and drove decent. But to get best performance and MPH at the strip, drilled both shooters to .035 and went up 4% (Edelbrock one step) in fuel on both ends of both carbs. O2 is a good tool, but you still have to try stuff.
Trans not shifting into 3rd well - that sounds like vacuum modulator, either you have really low vacuum in the intake or the hose/line has a leak.
It does sound like carb(s) issue. For fun, I have two same frankencarbs here - ProForm 750 DP centers, QFT blocks, billet 4 corner base plates, etc. Same jetting, same IFR (33 IIRC), same PV. Put one on the dragster - blubbers, breaks up at RPM, not the least bit smooth, sounds like it is loading up. Swap on the other - clean idle, clean above 3000 (big solid roller in the motor). Go figure. Says to me that there is something really out of whack with one of the QFT blocks. I have a ProForm purple block with the same deal - used it as the front block on a 750, never worked well. Changed to a stocker from another 750DP - ran well.