If it pops out of second gear, then there are some things to consider:
1) It is usually a case where worn parts and loose clearances cause this to happen. It is very common!
2) I've not found a single rebuilder that will guarantee their transmissions WON'T pop out of second gear on deceleration (especially from higher RPMs). Most will hem and haw a bit if you specifically ask.
So, it is kind of up to you to see if you can round up the best parts, set the clearances on the tighter side, etc..
3) Things I do: I have Charlie/NY re-bush my second gear to the specific main-shaft I will be using in the transmission. This is to get a slight "drag fitment" on the bushing. I've found that used gears and even NOS ones can be quite loose on the mainshaft.
4) Main shaft: I try to find NOS main shafts (or really nice used ones) - as any wear on the front bearing snout introduces a lot of play into the mix. Lots of guys don't mic the snout to see the wear - I always do. I also put the transmission input and main shafts in my lathe and see how much side deflection I get (with the caged roller I'm planning on using). Sometimes I swap things out to achieve the least amount of deflection where they meet in the middle. Of course, this requires that you have multiple sets to work with.
5) Mainshaft Caged Roller Bearings: I try to find NOS originals or the best used ones possible. Last time I checked, all the repop ones were not up to the quality of the originals. One big issue is with the hardening of the "cages" - the repops I saw did not have hardened cages like the originals - big issue for me!
6) Main Cluster Shaft: All the repops I have seen use inferior materials, are not hard enough and are .001 undersize. If VanPelt has any NOS ones, I'd sure use them. Or, he might have really good used ones. You can turn them over 180 degrees to put the worn side on the bottom - this does help with used ones.
7) Main shaft stack-up end-play: I setup my thrust washers and the resulting stack-up end-play to be about .0025. I never allow it to be over .004. Usually, this requires screwing around with thrust washer combinations, or surface grinding them to exact clearances or surface grinding the back of the 2nd gear to achieve the tight clearances. The tighter the stack-up thrust, the better.
These are the basics, hope this helps!
B&S