Grinding noise coming from manual transmission in 3-5 gears?

Maybe all you need is new transmission mounts. Or even simpler, when the transmission was replaced after the clutch job, they didn’t get it quite seated in the mounts correctly, and it has worked itself loose. I wouldn’t guess a transmission problem. Manual transmissions as long as they are not abused by aggressive shifting and the fluid level is kept up to the mark are usually one of the most reliable components on cars. Still, there could be something wrong with the clutch, and the transmission may need to be removed to inspect the clutch assembly. Provided the clutch hydraulic path is verified to be working correctly, and a visual inspection shows the transmission is sitting on the mounts correctly, first thing I’d do at this point is try tightening up the mounts, re-torqueing all of them to spec.

Dean, you must not give an unknown mechanic anything more than your initial complaint. Tell a shady mechanic that you have a bad transmission and he might agree, sure you do and I’ll give you a rebuild as you have indicated that you are mentally prepared to pay for it. Let the mechanic do the diagnosis. The trans “shaking” is normal due to the compliance of the rubber engine/transmission mounts and makes it possible for something to touch a heat shield to make noise. Get more opinions for sure. Any feedback on heat shield contact? Did anyone look to see how close an exhaust pipe was to a heat shield or other part? You must either confirm or eliminate this possibility. It certainly had two mechanics and me fooled for a while.

Wha who thanks for the feedback, very sound advice , I guess I’m just gonna ask around and see what people say and take it from there. Guy I went to yesterday couldn’t really be bothered…

At this point I’m wondering if the guy who installed the clutch used a pilot shaft to align the clutchplate when he bolted the pressure plate assembly over it.

I think opening it back up is the only way this is going to get resolved. The clutch installation, I mean, not the tranny.