Problem with shifter hitting the floor pan, need help

First thing I would check is to see if your engine is sitting as low as it can in the K-member. I have istalled new motor mounts before and really had to wrestle with the engine to get it to slide right down to the bottom of the k-member. You know the little slats that the motor mounts bolt into. Get them right down to the bottom if they aren't already. Only thing I could suggest.

You just put a new K-Member in aswell? or the tranny double hump cross member?

LOL yes I think you may have found your alignment issue. BTW did you ever get your car weighed?

I had something similar happening with my notch, especially with the UPR cat'ed X-pipe I was using. Under hard throttle, the whole drivetrain would torque over and the exhaust would lean up against the tranny crossmember, transferring a weird vibration into the interior of the car, even after I notched the crossmember out to clear the cat. The shifter was tilted a little too far over to one side, as well, but I can't recall if it was toward the driver's or passenger's side.

When looking at the motor underneath from the front with the car flat and level on pavement, I could see that the engine, itself, was sitting a little crooked. Motor mounts were getting worn and while they hadn't completely torn, they were permanently skewed to one side. I swapped 'em out with a fresh set of 'vert motor mounts and I suddenly gained an inch or two of clearance everywhere that it had been banging/rubbing on the exhaust before.

Maybe peek at the underside of your car on flat concrete and make sure the engine is sitting level in there (the hanging distance of the X- or H-pipe may or may not give an indication of its angle).

Also, is the new tranny mount you put in there poly or rubber? Switching to a poly mount on the notch made a HUGE difference in the shifter's feel - didn't flop, bounce, and bob all over the place anymore like it did with the stock rubber mount.