Weird noise after 4 speed install

Update:

Borrowed a slip yoke from a buddy. Fired it up and instantly, no sound. Put it in gear, sweet no sound. Then I could feel the trans shake, so I got out and observed the motor and it's shaking very intermittently just like before. So I think whatever is happening was traveling down the drive shaft and ending on the diff.

I don't know if it's a bad miss or what. I can't say that it did this before with the automatic, but I had such little drive time on it. It's a neutral balance 340 with the correct balancer and flywheel.

I don't know what an out of balance motor feels like, but I would think it be all the time.

What makes me.think its a miss is the header pipe temps are all over the place. I'm going to pull the plugs tomorrow along with the valve covers and see if anything is revealed. I dont hear any valve train noise.