I am going to try the clutch switch jumper and see if i can reproduce the problem in different gears. Thanks!I understand the thought that the neutral switch could stay showing neutral when in second. My suggestion was to force the neutral map by jumpering the clutch switch as a test. If you jumper the clutch switch, then all gears would use the same neutral map, and you would see whatever effect that map causes in every gear. If the problem still presented only in 2nd gear with the clutch switch jumpered, then it is not the map.
You could probably accomplish the same test by disconnecting the neutral switch.