Ah gotcha I misread that part. In that case run with the 3.55s now and get as much of the tuning (cam timing, ignition, carb) and diagnostics out of the way FIRST then see how it runs. No point in throwing more upgrades at the car if the current combo isn't working to its full potential. Get your engine tuned up proper and go from there.
Honestly if it was mine I'd be first doing a compression check, then pulling the timing cover (again), doing a full check with degree wheel of your cam timing and lift after lining up the sprockets dot-to-dot, then put it back together and move on to the ignition. If the cam checks out to be installed correctly my first move would be to crank up that initial timing and see if it idles better without so much of a drop shifting into gear.
