Check the fluid level in the transmission. My truck is an 89 with the same transmission. It will have a 5LM60 if it is the original trans. They take two quarts of synchromesh fluid. Get the stuff found here
http://www.ebay.com/itm/161475758781?_trksid=p2057872.m2749.l2649&ssPageName=STRK:MEBIDX:IT
You can also find the fluid at your local NAPA or auto parts store.
I will tell you, this transmission is a little notchy, it shouldn't make those kinds of noises though. If it makes noise when you push in the clutch, the throwout bearing is likely bad. My trans is a little notchy and has 150k miles on it if that is any consolation.
Anyway, the fill hole is the plug on the passenger side of the transmission on the picture below. The drain is on the bottom of the transmission. Both take a 17mm hex head to remove it. My advice is get a bolt with a 17mm head on it, put a nut on the threads and weld the nut to the threads. Then you can use the head of the 17mm bolt as the hex head, much cheaper than buying one.
Drain the transmission by removing the bottom plug until it drains completely. Replace the plug and then pull the side fill hex head and fill it until it starts leaking out. Take it for a drive afterwards and see if it is any better.
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