Anyone run into any clearance problems with first gear rubbing against the differential when tightening done the tranny case.There seems to be no clearance between the gear and the diff.The tranny is JDM type R so all I should need is the shaft and ring gear.

 

I don't know about the ATS set specifically, but there isn't much clearance between the 1st gear and ring gear until the countershaft is pulled up and held in place by the snap ring during assembly.