So, this will likely go in my upcoming build thread but I figured it would get more traffic here. I think I've figured it out but I want to make sure I don't jump to the worst conclusion.
Last week I picked up a 2002 Toyota MR2 Spyder with 98k miles. No clue on if it's ever had a clutch, but the clutch takes up right off the floor, so it was either replaced at some point or the previous owner was very gentle on the clutch. While test driving it, I noticed a faint clattery noise from behind me while accelerating or decelerating. Steady speed on flat ground, or idling in neutral, or with the clutch in, and the sound goes away. Looked under it and there was no fluid leak, so that made me feel better, in that the transmission likely hadn't been run dry. My first thought was, since it had the original 21 year old accessory belt and 15 year old tires, maybe a fluid change would help it. Changed the fluid on it on Saturday and the noise is still there. It had the correct amount of fluid, and while there was some metal flake in it, it wasn't like silver paint. I figured that with likely 21 years and 98k miles on it, it looked acceptable.
The car shifts fine, doesn't vibrate, and once you get up to 55mph+ you can't hear it over the wind noise with just the windows down. The fact that the noise goes away when I push the clutch in makes me rule out pilot bearing and throwout bearing. The fact that it doesn't make the noise in neutral with the clutch engaged makes me think it is on the input shaft of things.
I'm leaning towards output shaft bearing, especially since doing some reading on SpyderChat it sounds like the C56 transmission was somewhat prone to those failing. Guys say they've had them replaced at less than 100k miles for the noise. I should add that the LR axle appears to have a boot that tore from dry-rot and has thrown quite a bit of grease out. I suppose that could cause the issue, and I do plan on replacing it.