If it is only doing it under load can you make it go away by doing anything else? For instance depressing the clutch?
Is it just a noise or is there a vibration there as well?
Assuming you know what a bad bearing sounds like (growling, metal on metal noise), can you rule this out?
Believe it or not, the 3650 (as well as the T45) are a
little noisy by nature. It is just the way the gears are cut and the makeup of the syncros and blockers. Have you tried checking the fluid level? In '03, Tremec switched from non-synthetic ATF to a synthetic ATF, like Mobil 1. What fluid are you using? Pull the fill plug out (side of the main case) and see if the fluid level is correct. It should trickle out when the plug is removed. If it does not, stick your little finger in there and see if you can feel the fluid level. If not, add some fluid and see if that helped.
When is the last time you changed the fluid? If you haven't, I would try that first.
The "clunking" you mentioned also has my mind going in another direction all together....

Have you checked your u-joints lately? A bad one will cause the clunk you described, also would cause noise and a vibration if it is bad enough.
Richard
Tech Support
Tremec TKO, T45 & T56 Transmission Systems