Need help diagnosing transmission noise

I need help identifying sources of noise/vibration in my RX7. I believe they originate with the transmission. It's a naturally-aspirated FC transmission with Miata guts stuffed inside. I had a shop modify the input shaft and I reassembled everything myself. Ever since getting the car back on the road last August I've had several distinct noises and/or vibrations:

1. Whirring/rumbling noise in neutral with the clutch engaged (pedal up). This noise goes away when I disengage the clutch (pedal in). I'm nearly 100% the input shaft bearing is bad since I can hear the it spin up to speed when I engage the clutch.

2. A similar noise to (1) but while driving in gear. It's by far most pronounced in 4th gear while cruising but I've recently noticed it in other gears as well. It seems to go away during acceleration/deceleration. I'm thinking this is also likely a symptom of a bad input bearing.

3. A vibration/resonance in 5th gear. The best I can describe it is that it's like an imbalanced driveshaft/wheel or flat-spotted tire  but it only really occurs in 5th gear. It really picks up around 65 mi/hr at 3200-3300 RPM and is at its worse somewhere between 70-75 mi/hr and then starts to taper off again. I don't think it's a driveshaft/wheel imbalance or a flat-spotted tire because it goes away if I downshift into 4th. It'll literally be smoothly buzzing away at 4000 RPM in 4th and as soon as I upshift to 5th I get "wompwompwompwompwompwomp" I think I've also occasionally felt it, to a much lesser extent, in 3rd gear at even higher engine speeds (>4500 RPM).

4. This is probably related to (3) but every now and then I get a weird arrhythmic vibration while decelerating in gear. It's the same low, heavy, drone but at irregular intervals. It might do something like, "wompwomp... woooomp... ... ... ... wompwompwomp" and then stop.

Like I said, I'm fairly confident (1) and (2) are because of the input shaft bearing. So much so that I already have replacements and am just waiting on a free weekend to pull the transmission. (3) and (4) have me stumped. I've extensively searched all RX7 and Miata forums and haven't really come across something similar. I also plan on replacing the transmission rear bearings and rechecking/resetting 5th gear end play while I'm in there.

Throwout bearing could also explain (1)  The rest is internal manual transmission voodoo and I'll leave that to the experts.

Pilot bearing in the input shaft where the main shaft connects up.

In reply to Curtis :

Wouldn't that be the case if the noise occurred when the clutch was disengaged (pedal in)? Otherwise, the throw-out bearing isn't spinning, correct?

In reply to Ranger50 :

I suppose that could also be the source of the noise in neutral for (1). What about (2), though? In 4th gear the input shaft and main shaft are moving at the same speed so that bearing is just along for the ride.

Yesterday I went for a quick drive and the noise and vibration are definitely being caused by the transmission. Disengaging the clutch causes the noise/vibration to go away even while maintaining vehicle/engine speed. I'm pretty sure this rules out the engine, wheels, tires, driveshaft, and differential. At this point I'm planning to bite the bullet and pull the transmission apart again. This time I'll replace all the bearings and races and make sure all end play is in specification. Previously I had reused parts that "seemed fine" and a reused all the spacing washers under the assumption that everything was okay to begin with. In hindsight, this probably wasn't a good idea with a junkyard Miata transmission. I'd like to go back and smack my five-years-younger self in the back of the head.