I just installed a SBC double disk in my 99, I changed the input shaft to the 1 3/8 shaft and everything slide right into place with no trouble, then I was ready to instal the transmission ,but after getting the input shaft into the clutch splines the transmission slide up and stopped about a 1/4'' from the bell housing and I had to pull it on up with the 4 transmission bolts and it was hard the whole way, I also checked the 5th gear nut and forgot to completly tighten 2 bolts on the 5th gear housing/ I took the truck for a drive and it shifted smooth and the clutch engaged and disengaged good but I now have alot of transmission growling especially in 4th gear and I tightened the two 5th gear case bolts and it didn't help what could be the cause did the 5th gear housing maybe get slide out of line, it looks fine though, what could be the cause

 

any ideas?