Note: The following is related to 39-48 transmission setups . . . not the earlier stuff!
Given the discussion is about the transmission popping out of second gear, there is a lot more to think about. What I've found is that the issue is primarily related to tolerances/slop in the overall transmission setup.
I pay particular attention to the dimensions on the main-shaft (the front caged roller bearing area) - it needs to be as close to the original specs as possible. If the bearing area is worn, this can really contribute to the problem. I do not run worn mainshafts in my rebuilds . . . I cherry pick the best ones I can find - in many cases NOS ones.
Also, I believe that having any slop in the fitment of second gear to the main shaft is also an issue (and this is common!). I've been working with Charlie NY and having him re-bush all my second gears - for an exact/tight fitment to the specific mainshaft I'm going to use (I send him the complete mainshaft assembly).
I have built two 39 trans with Zephyr gears in the last couple of years - with perfect mainshafts and the newly bushed 2nd gears and they do not pop out of second gear (even under hi-rev abuse). Just try to get anybody who rebuilds these transmissions to guarantee they "won't pop out of second gear" . . . good luck with that!
. That is why I build my own. (Am building four 39 boxes when I get back from vacation - all are setup as I note in this thread).
Another area that I concentrate on is having a really good cluster shaft - either original Ford stuff, or I make my own. All of the repop shafts that I have bought are undersize - usually .001 to .002 . . . which adds slop to the cluster setup. Also, when I stack my gears up on the mainshaft, I setup the thrust clearance to be exactly .004 - the lowest end of the spec.
I've found that the tighter you run ALL the clearances, using the highest quality parts . . . the better. As a youngster, I always put up with my 39 boxes popping out of 2nd under high revs and deceleration - as an "Old Goat" I now try to build transmissions where I don't have to hold them in second! LOL
Hope this helps! B&S