Need help with transmission rattle

The manual transmission in my 98 Tacoma with 159,000 miles on it has developed a rattle that has gotten the best of me, at least for now.

The first thing I did was replace the exhaust heat shield. No help. Next, I replaced the drive shaft. Still rattles. Then I had the transmission rebuilt. Still no help. The transmission shop was able to isolate it to the transmission by running it on the rack with the driveshaft disconnected. Now's here the catch. It starts to rattle when cold after being driven a mile or two, then stops once the engine and transmission reaches full operating temperature. And when it rattles, it does so with the clutch in or out, which tells me it's not coming from the engine, or at least I don't think so. I can also feel the rattle in the stick (clutch in or out). And like the rattle, this goes away with the rattle once the engine and transmission reach peak operating temperature. It rattles mostly in third, forth and fifth gear and doesn't follow engine rpm. It sounds much like a loose pan rattling inside the transmission.

Could this be as simple as a bad speed sensor? The speed sensor is mounted near the end of the transmission housing and near the drive shaft?

I could have made a down payment on a new truck for what I've spent trying to find this annoying rattle. Any and all suggestions welcome.

Oh yeah, I tried another catalytic converter as well, soon after replacing the exhaust heat shield.

Thanks,

Dan