So, I have my ATL2 back to a working state, in no small part thanks to Fred.
When I started I had the same problem as a few people have had here, a 5v power rail shorted to ground through a bad 10µF tantalum capacitor on the interface control board (94 015) at C27. I would strongly suggest anyone replace this capacitor on their board.
I also had a bad value ceramic cap at C33 though this seems like an unusual failure and I'm not sure it was actually a problem. I doubt this is common.
After getting that far I then spend a while chasing down a problem with the 24v rail and traced it to a 1µF tantalum capacitor at C7 on the Interface Board Control Head (94 017), also shorted to ground.
As you can tell, there's a bit of a theme with failing tantalum capacitors here and I don't think replacing all of them would be the worst of ideas.
The third problem was really annoying, after realising that the ferrite disc had broken off the rotation motor I glued it back on but still had an error where the motor would immediately start freaking out and changing rotation rapidly. Turned out the previous person who had (badly) taken this jobo apart had connected the hall sensor for that motor in the wrong socket and I had inadvertently put it back in that same wrong place. It should be connected to ST9 - Mot. Sens. at the bottom of the board but it will, wrongly, fit in ST3 in the middle.
The fourth problem was the motor speed, I got 50 and nothing else. After pulling almost all the capacitors on the transformer board signal chain and finding zero problems I followed it back to the 74HC374N flip-flop at IC8 on the control board (94 015). Changing that chip which is cheap and easily available (in my case for a motorola non-n version, which is a direct replacement part) I got motor speeds back.
After a short detour wondering why I broke the pump, then realising I had swapped the motor and heater input wires reassembling the transformer board, it worked!
I along the way also had to find a lot of replacement hardware, something like half the fasteners on my machine were missing. They are all metric and for the most part stainless steel, though with some brass bolts on the base unit. These aren't all of them but are the ones I needed.
– Cheese head brass slotted M3 × 8mm for the base unit
– Countersunk stainless slotted M6 × 40mm for the lift head
– Countersunk stainless slotted M5 × 12mm for the lift head front
– Countersunk raised head Phillips stainless M3 × 8mm for the front panel plastic
I still need to design and build myself a chemistry recovery funnel, if anyone can submit some photos and dimensions of those I would be very grateful.