Guys, needs something cleared up. In the following pic is a JDM S80 ITR 4.7 FD transmission. It has an enclosed bearings with the differential. Do these come with a shim under the differential in the clutch housing side? Because we just took apart the transmission and we are not sure whether we misplaced this part.

 

No. The shim is in the transmission case not the clutch housing.

 

Actually we took this apart a transmission to install Mfactory 3rd - 1.652, 4th - 1.296, 5th - 1.00 close ratio gearsets and new oem 3-4 synchros, springs, hub and sleeve. So we fixed everything thing up, all gears aligned and turned up freely, shift forks lined up etc. Finally got the c-clip on the bearing groove and tightened the housing. But after tightening the housing bolts the input shaft wasn't moving freely, it was turning with resistance and after a half turn, it gets harder and then loosens a bit. Changed into different gears and checked, it was still the same. But if the bolts were loosened it turns somewhat freely. What could be causing this?

 

Incorrect assembly, mainshaft not shimmed, countershaft not shimmed. One or more of those.

The ratios you're running don't require any clearance work to the case just in-case you were wondering and hadn't looked into it.