Transmission going bad?
 

Whenever I have the tranny in nuetral, and the clutch let out, I hear this god awful rattling. I know the input shaft has some wobble to it. I replaced the clutch earlier this month and noticed it. Is this something that can be fixed or should I scrap the tranny? thanks!

The input shaft is supported at the other end by the pilot bearing.

Does the transmission make any noises in any other gear?

It's mostly in neutral, but in other gears at low RPMs I hear it. It's actually chewing up my pilot bearings. There was almost nothing left of the last one i took out.

When I replaced my clutch in my 88 N/A it made a god awful grinding sound for about 5,000 miles. If finally fixed itself. Just my exp.:)

Mine made that sound a while before I replaced the clutch. I did the pilot bearing too, there was nothing left of the old one. I noticed the shaft had a good bit of wobble to it, but thought the new pilot bearing would fix it. It did, for about a 1000 miles. Now it's doing it again. So what I'm thinking is the shaft is just ripping apart the bearings.

Well the only thing to do is take it apart and see. You could just drive it and hope nothing happens. If the tranny breaks it's not to expensive to get a used one.

Is there a way to tighten up what is loose?

Pilot bearings are very hard to damage through general use. They mainly get torn up through improper installation (of the bearing or transmission).

For what it's worth, I used to get horrible sounds like that on my nonturbo right before the transmission completely shit on me. Chunks of metal in the fluid when I drained it. But I had abused it through a lot of hard drag launches.

bearing
 

Sounds like a bad input shaft bearing. I am currently fixing the same problem.