new project and honda civic questions

Last Friday I picked up a new project off of CL-a '90 Civic Si hatch, 166k miles, runs and drives and has some nice aftermarket parts. All in all, a nice score for $400.

The only problem it has that keeps me from tagging it and driving it every day is a howling noise coming from the transmission.

-It's medium frequency/pitch, seems to be unaffected by whether the clutch is in or out or what gear the car is in, and only heard while moving. Loud enough to be audible over radio and conversation. It seems to get a little louder under heavier load (i.e. if I stab the throttle).

-It's intermittent, and I can't seem to figure out what triggers it and what makes it go away. The trans makes the noise more often than it's quiet.

-Other than the noise, the trans shifts fine. Clutch is good. Trans is full of oil.

I don't think it's a throwout bearing, because it doesn't seem to change if the clutch is in or out. I'm thinking maybe a bearing in the transmission, but I'm not well-versed in transmissions and have no idea.

Any ideas? Are there any endemic problems with the transmissions in these things?

Input shaft bearings are common, but from your description that's not it. If you chose to rebuild, I'd recommend a kit from synchrotech. About $250 for everything including diff bearings. I just rebuilt a single cam trans last night with a kit from them, the bearings are all own NTN and the seals are all OEM Honda. Otherwise a junkyard trans might be cheaper. IIRC, the only difference between DX and Si transmissions is the final drive, so if you are comfortable rebuilding and have access to a press you could swap your ring gear and countershaft into a DX trans and have and Si trans for the cost of a DX.