With the clutch in the rattle is not there but when I release it the rattle starts again. Also while in gear it sound terrible past 3000 rpms in first and second and don’t really hear anything in any other gears. After reading a bit it seems like it’s the input shaft bearing . Does that seem like the problem?? And whether it is or not how soon should I replace it, if not what’s the next thing that’ll go and how will I know. Sorry for the bunch of questions but I’m struggling here

 

I had a similar issue. The rattling was more like a squeal in my case. My throw out bearing was seized with rust.

New clutch and bearing took care of it.

 

Does sound like a throw out bearing but I'm not sure why you would only hear it in specific gears.

Usually bad or plain old abusive manual driving will ruin these bearings.