I have a 1988 GMC Sierra 4x4 truck, and I recently bought a rebuilt NV3500 transmission from a 1995 chevy truck (I picked this year, because from 1993 onward, this particular transmission used a single shift rail and a better bearing design as opposed to the older designs which were prone to early failure), which should bolt right up to my truck. The transmission bolted up to the engine fine, but I noticed that when shifting, there was a slight delay before the transmission would shift into gear. It's like when I am shifting, I am temporarily being blocked out of each gear for a few seconds (especially 1st and 2nd gear) before it decides it wants to go into gear. Keep in mind, there is no grinding noises or anything like that.
At first I thought maybe the hydraulic clutch system was faulty, which shouldn't be the case, since everything is new. I bled the master/slave cylinder of all air bubbles, but it still did nothing. The clutch and pressure plate are also new, along with the pilot bearing, clutch fork, release bearing, etc.
I had a mechanic take a look inside the transmission and he said all of the synchros were new. So I am basically at a loss ... what could it be?