Did you notice a change going to the 3.90?
I'm going for the 3.38....but, one thing at a time...
I noticed a huge difference but I changed to the 3.90 the same time I changed to the T5 Trans. I do know that if I'd run a 3.38 instead of the 3.90 I would never get out of third gear. You'll have to pair your rear end to whatever transmission you will use, also taking tire size into account.
The center section or "guts" will work from '55 up to '61 or '62, just make sure of what you're getting. I'm using one from a '61 1/2 ton that had a 350.