Take it back to the shop that built it...If there's truely no electrical problems that would be putting in limp mode then there may be a problem inside the case. If you pinch the green o-ring at the base of the forward drum, you'll have third gear starts. You should still upshift to 4th in such a situation so if you dont upshift at all from 3rd to 4th its not as likely.
Its all just a guess from here, of course but if a shop took that thing out, rebuilt it and put it back in, let them deal with it. Its either a short in the transmission's electricals, vehicle harness, tcm/pcm or some other sensors that are throwing off the tcm's command and contol of the trans (MAF and TPS are a couple examples) or a problem in the forward drum.