Scary sounds from TR-3650 Anyone else hear this?

I have a TR-3650 in my 99gt. was installed with 10K miles on it.
Here's my problem:
At idle in neutral, it makes a low rattle noise (very similar to a shaft with a loose bearing that is wobbling) it is NOT the throw out bearing.

In gear, when at low RPM's (under 2K), when I floor it it make a loud rattling noise that goes away around 2.5K.

even worse, when driving in any gear, getting on or off the gas allows you to feel lots of gear clash along with a metalic clunking sound and the car jerks back and forth like when my girlfriend tries to drive it.

I have an aftermarket shifter and urethane mounts, but still, it shouldnt be this noisy or loose. Is this normal?

Do these trannies (normally) have that much free play inside them?

I'm running B&M synchromesh in it and it shifts fine (i guess, I've never driven another TR-3650) and does not grind. However, sometimes it will lock me out of 3rd on slow normal shifts, but only like once every few weeks. Probably me just being lazy and not lining it up right.

Should I be saving for a new tranny?

i did do a back yard gear change a while ago. Gear lash was in spec. And when I replaced the Diff a few months ago the gears looked fine.

When I was under the car, I put the tranny in 1st gear (parking brake off so wheels can spin) and wiggled the drive shaft, in theroy, it should not turn. in real life it should have minimal lash. I could rotate it back an forth about 1/10th of a full rotation and it mad the clunk sound.

I did the same to the rear end with the tranny in neutral and parking brake ON. Lash was only like 1/50th of a turn.

does anyone know the ford specs for this?

or just if it is normal or ready to fall out.