UPDATE: It's working!
I swapped the X & Y MPSU07/57s and got a partial vertical collapse. I had some TIP31C/32Cs, which had similar enough specs that I figured I could use them for short-term testing. In theory they would have worked if I'd bothered to check their pinout, which is BCE instead of CBE. I got too anxious to see a real image that I checked the screen first. After a few seconds of nothing, I returned to the back of the machine to see one of my resistors (R7) glowing white before it popped. It may have even actually flamed out, but I was scrambling to get to the power switch and I'm not sure. Another resistor (R12) burned out, too, along with F1.
Whoops.
So I replaced the resistors and put the original MPSU07/57s back in to verify operation. Same problem, but it was working that far. Then I grabbed some BD139/140s, which have been recommended as replacements here on the forum. I *swear* I put the pins in the right order, but after putting those in and powering on, BAM!, same 2 resistors popped. This time it blew F3 and F4.
Yay! More mistakes to learn from!
So I ordered some original replacements from Andy's Arcade on eBay. While I was waiting, I replaced the fuses and put the originals back in, to verify it was working as expected (with the 1/2 horizontal collapse). At some point I replaced the 0-Ohm resistors with jumper wires. Several of them tested bad when the game was live, but replacing them didn't have any effect that I could see in the board's current state.
New transistors arrived today and after getting them in, the game woke up working great. I went through the size and alignment procedure and got it dialed in. I had to bump the brightness quite a bit, but I don't know if the HV was with this Amp or not.
There's some pretty bad pincushioning on the test screens, but it wasn't really noticeable during the game.
The raster test screen was also skewing a block of red lines to the right as it got lower. The manual says it's used to adjust white tracking, and the picture shows a rectangle, not a trapezoid. What could cause that?
Lastly, some of the lines were "bowed", which is especially noticeable with text. There was Tech Tip that mentioned something similar, but I'm not sure if it's the same thing.
Even so, the display was absolutely stunning and an utter joy to view.
Thanks everyone for the help. I'm open to any further suggestions.
I am curious,
@andrewb, what are the downsides of the Atari and/or Michael Kelley (et al) upgrades? I haven't replaced the 2N3904s in Q11/12/13 & Y equivalents. I'll have to order them.
I've half a mind to fab a new board with the fixes/upgrades as jumper-selectable options to be able to A/B them.