Be sure you got the correct input bearing, it should be the wider of the two for a 5spd input shaft. I believe it is a 24mm bearing, the auto's use a 16mm bearing.
I just ran into a similar problem when I did my 5spd swap. I have a DHD and the guy I bought the tranny and parts from sent the 5spd input shaft with as well. But ever since I changed the input shaft I have had a problem with the transfer case kicking into neutral and making a high pitched grinding noise.
Well we took it all apart, as well as a DLD from a 5spd and found out that I had two problems. The first problem is being an auto truck with a one piece tail housing (DHD) I had the 16mm bearing not the 24mm that I needed for the 5spd input shaft.
The second problem was the input shaft I have is for a 241HD which is a HD without the PTO gear so the input shaft is an 1/8th inch longer than the normal 5spd input shaft for a DLD and a DHD (w/PTO gear).