Changed out my clutch, flywheel, and trans fluid during an engine swap I just did. Used Torco MTF. All the rest of my drivetrain was working great before the car went under the knife. Now when I'm driving, when I give it some gas there is a deep rumbling noise coming from the engine bay. Doesn't happen when I'm off the throttle and moving, or revving the engine while stationary. Funny thing is you can hear it better with the windows rolled up than with them open. Axles and boots are in good shape, transaxle is locked in and I refilled its driver side mount with bearing grease. I'm positive I torqued everything according to the Helms manual when I installed the Exeddy clutch and 13lb flywheel. I'm at a loss on how to diagnose this issue because I can only seem to hear it while driving. What are some things I can do to narrow down what might be causing this?

 

Dropped the trans and looked at the clutch setup. Nothing visibly wrong. Engine mounts are in good shape too.

 

Alright, so I figured out how to get something while stationary. I put the front end on jackstands and started the engine. If the shifter is in neutral there is no noise from the engine when I rev it, sounds great. However, if I shift into gear there is a God-awful rattling noise from the bellhousing area. I can hear it the loudest in 5th gear. The noise isn't constant, it comes and goes by the seconds, and releasing the clutch doesn't seem to affect anything. So would that rule out the throw out and input shaft bearing? Does this sound like a rebuild is necessary?