90 Ranger Trans Noise

I just replaced the clutch, slave cyclinder (with bearing) and hydraulic line on my sons truck. The clutch needed replaced and there was a noise comming from trans area witch went away when the clutch pedal was depressed. This noise went away after the replacement but shortly returned only louder. Advanced Auto said it sound like throw-out bearing which is new. I don't want to start this nightmare again of removing the trans. and EXHAUST. We ended up cutting the header pipe and having it welded back. There appears to be gear oil leaking from the rear seal of trans where drive shaft enters. My thought was that oil is leaking out and I am hearing gear noise???? ANYONE HAVE ANY SUGESTIONS??????