@Sam Harris, my NVG246 (NP8) has a very distinct (read: loud) clunk when shifting in and out of 4lo, and it's always been that way, even before the rebuild. The dash light thing happened to me maybe a year before the TC was rebuilt; I'd be going down the road and the switch would suddenly show "N" but I'm still getting power to the wheels. Pulling over and turning the key off and back on would usually correct it for a while. Replacing the encoder motor fixed that, so that would be my first guess. You could check to see if they got the bolts tight on the encoder motor.
The dash switch can be removed and ohmed; if you need that info let me know and I'll post it or reply to a PM.