Lsssleeper Coupe

OK I have searched and I need more help. Ok here is my problem I was given a 1990 ls motor that was auto I converted it to manual transmission. A friend gave me a Ys1 tranny for a gsr. I bolted it up and everything and when it came time to bolt up the intermediate shaft THe bolts did not align. It was a small budge on the block the did not allow my 1990 interemdiat shaft to bolt up it was getting caught there. I read on a forum to shave down the block to allow for the intermediate shaft to bypass this problem. I have been to the junkyard and tried a 88 intermediate shaft and it fit but did not bolt up. the pattern on the intermediate shaft was way off. I am stuck on this. THe motor again is a auto block converted to a m/t it is a ys1 92-93 and it does not bolt up to the block. Can someone help me please.