Not sure if there's a flow chart, but your approach is actually pretty spot on so far. Connectors and voltages. I'd probably start with the power supply board, you'll want to replace the electrolytic caps there. The bridge rectifiers can be tested with a dmm using the diode test. Coils under the playfield can be tested for resistance, typically anything under 2 ohms is bad (though not always).

It sounds like you have a few different things going on right now, so I'd start by rebuilding the power supply (electrolytic caps, check for correct fuses, etc) and connectors (re-flow/replace as needed for male and female sides). Once you have good voltages and connectors, you might find some of the other problems go away.

A lot of times it can be a transistor that went bad and is permanently "locked on" providing a path to ground for one of the solenoids, causing the 2.5a slow-blow fuse to blow after the game's been on a few seconds.

With the game off, I would start by disconnecting all 3 solenoid connectors on the main cpu/driver board, as shown in the chart below: 1P11, 1P12, and 1P19 (on the board, it may be labeled J11, J12, J19). Replace the 2.5a slo-blo fuse (make sure to use *only* a 2.5a slo-blo aka MDL fuse--don't go higher than that). Turn on the game and see if the fuse blows. Listen carefully to the game and watch the playfield to see if you catch a coil activating immediately when you turn the game on. If it doesn't blow, try plugging in one of the 3 connectors and see if the fuse blows. You may even see a spark at one of the connector pins as you plug it into the board--that may give you a clue as to which transistor/coil is locked on.

If the fuse doesn't blow with all 3 solenoid connectors plugged in, see if you can run the coil test in diagnostics and see if any of the coils blow the fuse when they're supposed to fire.
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That's so funny you found a fuse causing the problem like that! For all the times a seller claims the problem is "probably just a fuse"

The 2 non-working switches share a column on the switch matrix, column 5. According to the chart, they will have a green/black wire at each of those switches. Check for the green/black wire(s) and the 1N4001 diodes going to each of the non-working switches. Also check the green/black wires and diodes on each of the other switches in the same vertical column on the switch matrix chart here. Make sure those wires and diodes are tightly attached and wired properly to all 8 of the switches (start with the trouble switches and move over to the others if the problem persists). A broken wire or diode on one switch can sometimes cause problems elsewhere on the same column or row of switches. One easy way to tell if there's a break in the "daisy-chain" in the green/black circuit for column 5 would be:

set your dmm for continuity test
put one lead on a green/black wire going to a non-working switch
place other lead on the green/black wire on the other working switches from that column and listen/check for continuity
You should have continuity between all 8 switches' green/black wire. You should also have continuity from the green/black wire on all those switches to pin 5 of connector 1J8 at the driver board (check the switch matrix chart, column 5)
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Check the switch ganged up with the end of stroke switch, like gutz said above. It sounds like the wiring lugs on the switches may have gotten mashed together or the actuator broke or something else causing the switch to keep activating (causing the revving sound you were hearing)

Sounds like you're getting close to the source of the problem, possibly...

I would also recommend checking the associated transistor and predriver transistors on the driver board that control that coil. It's possible the transistor(s) locked on, frying the coil. If they're bad, they'll fry the new one & blow the fuse again.

Ah, good catch! I hadn't checked the schematics Does it seem likely then it was a bad diode that fried the coil?