Drivetrain M-7003-Z T5Z trans

Hello all. Noobie here. Ok so some back ground on the power plant. I have an 82 TTop GT hatch that I converted over to a full roller, eagle 331 stroker kit mahle pistons .040 over Ford X306 heads B CAM edlebrock intake and 650 carb.

I decided to put a T5Z in the car to get rid of the old SROD 4 speed. I bought the Trans and T5 bell housing from American muscle it was delivered last week, I installed it with no issues after driving only 50 miles I was leaving a red light and heard a pop sound and then clanking coming from the transmission. I got the car home and pulled the cover from the clutch arm to see if maybe the throwout bearing or Arm was out of place. And as I thought they were in place and assembled. Clutch is nice and smooth bearing is working properly as I had a helper to crank the car as I viewed the throwout bearing and also had them depress the clutch a few times. This clanking noise can be heard while in neutral if you Rev the engine to 2- 2500rpms. It makes the noise in every gear, but the transmission still shifts smooth and is transferring power as it should just with a clanking noise. Has anyone every heard of a brand new transmission doing this while still in break in period?

When I dropped the old Trans out I put a new clutch and pressure plate on. New throwout bearing and clutch arm. I also didn't think it was in the Trans at first thats why I pulled the cover for the clutch arm to check all of that first but you can hear and feel a nasty clanking and vibration through the shifter and floor board if you lay your hand on the floor board. I know it's hard to diagnose what's going on without seeing or hearing it, but what are your thoughts monkeybutt2000?