Is my 904 toast?

Last night at the drag strip, I experienced a sound/feeling that spelled bad news.
It was my 5th run of the night and somewhere in 2nd gear I felt and heard a big vibration and shaking, can't really call it a grind but it was hard to really hear over the engine and the guy next to me. I felt nothing in 1st and it went away when I shifted to 3rd. My ET was right around where it usually is: 12.52", so it was certainly pulling like normal.

Below are the specs of the car and then the history of this transmission:
1973 Dart Sport 340 body (everything else from my '73 Duster)
380/360 Mopar Magnum crate engine
3000 stall Hughes Performance TC
Transmission cooler (not using radiator tank)
Reverse manual valve body
3.92 rear gears
Mickey Thompson slicks

I typically run the electric fan to keep the transmission as cool as possible right up until I stage. Then I turn it off. That said, it was 54 degrees at the end of the night and the car had been sitting for about an hour.
I do a good burnout and typically launch at about 2500 rpm and shift between 5500 and 6000.

History
The engine and transmission came out of my previous race car ('73 Duster).
The driveshaft and rear end were rebuilt for this version.
I had the original transmission rebuilt about 5 years ago by a local guy, no longer in business. He put in a TF-2 kit and did a stock rebuild (no special high end stuff).
It never really shifted as hard or as accurately as I liked.
So two years ago I put in a bigger stall converter and the reverse manual valve body and saw big gains on the track with super tight and accurate shifts (no slop between 1st and 2nd like before).
Last week I changed the transmission pan gasket and put in new fluid. There were no chunks or anything in the fluid, maybe a little cloudy.

Previous concerns:
The Duster (previous incarnation) always had a weird, almost harmonic vibration while cruising in 3rd at about 2300 rpm, the pulses would get faster and then fade away upon acceleration and slower/fade away when decelerating. It was most obvious on the highway. I had the driveshaft rebalanced and it didn't change. I didn't know if it was the rear end or the transmission but don't think it was the engine.

In the current car (Dart), the vibration was much less present but I think it was still kind of there. That ruled out the rear end, as it was a totally different everything from housing to gears to new axles. But I never did much street driving as it was set up for the track, not registered or insured (and looks like it - the car begs to be pulled over!).

It ran strong all last year, never a hint of a problem, and super consistent.

This spring, after sitting all winter, when I started it, it was rich misfiring very badly and shaking like crazy. It even shook some wires loose. When I got that taken care of (choke adjustment), I heard a lot of clattering from underneath. I finally located the source of the problem: 3 of the 4 torque converter to flex plate bolts were really loose. I locktited them and torqued them back and the car ran/felt/sounded perfect again.

Last night was my first night back at the track. First run was totally normal. I had a missed shift on my second run, where I skipped 2nd gear and hit 3rd instead. I immediately shifted back to 2nd, tached up as normal, and went to 3rd. Nothing felt out of the ordinary. This is the first and only time I've ever done this.

My third and fourth (next two) runs were perfectly normal and the car is extremely consistent.

Then on the fifth run, I experienced that shaking. The drive back on the return route felt normal, but I was only going about 25 mph.

So here I am. I realize that I've been beating the snot out of this transmission but wanted to throw this out there to see if any of your gurus had any thoughts or ideas. Thanks in advance!