So I want to stay out of this thread but I think it's important that potential confusion be cleared up.
The following is obtained from the Williams manuals but be aware that the Williams manuals are known to have errors. The power supply board is D-8345 and unfortunately when Williams changed components used on the board as listed in the manual they didn't change the assembly number.
- F-14 and prior the manual lists Q1 as SDS201 and Q3 as SDS202 for the power supply. These are TO-202 form factor. The legs are EBC - emitter / base / collector.
- Fire! and after the manual lists Q1 as MJE15030 and Q3 as MJE15031 for the power supply. These are TO-220 form factor. The legs are BCE - base / collector / emitter.
This image is from a Big Guns power supply. You can tell because the stickers show "557" as the game number. This power supply has MJE15030 and MJE15031 installed. They used the straight pads (at the top) that are configured as BCE. The staggered pads (below) are configured EBC (you can follow the traces and verify this - the E trace is on the back side of the board).
Somebody has definitely rebuilt the high voltage section of the OP's board. That is obvious. I don't think the cause is incorrect MJE15030 or MJE15031 installation. Of course there might be something obvious on the back side of the board. That is what most people do. They hide their sins on the back side of the board so they are not visible. Other than that ... you will need electron vision to find faults in electronic components. This means you will need to measure with a DMM.