Were you able to get it into second gear with the shifter in place, but out of the car, before you rebuilt it? Is the shifter a cable arrangement, or does to operate the shift rails directly, like a ball and cup arrangement?
Is this your shift pattern --
1 3 5
2 4 R
If the reassembly fixed it, it was likely a fork/shift rail missalignment on the 1-2, or possibly the 3-4 shaft, or both. At dead neutral on all of the shift rails, you have a very small margin for error to assure you don't lock out across the gate. If the transmission is loose or worn, you may be accessing first gear while the 3-4 rail is not completely disengaged.
It's sometimes tough to tell if the issue is in the alignment or the shifter. It gets goofier and sloppier if you have an external shifter not directly moving the shift rails. At that point, not only does the transmission need to be dialed in, the shifter does, too. If both are sloppy, the stacked tolerances start to raise their ugly head.
The reason I brought up the issue of operating it under a load, is that if your case is compromised, you may never be able to recreate the problem on a work bench. You'll never be able to apply the kind of force that comes into play.
Chris
