Hmm... Was the game working previously? It's quite possible the schematics are incorrect. Williams schematics are known to have errors.
So, if it was working previously we can assume that the wiring is correct since that didn't change.
On the connector that was plugged into J501, check that you have 18VAC between pins 4 and 6. I believe that you have correctly checked all of the other pins.
If that all checks out, then the next step is to replace that C11 cap that blew up. Once that's done you can plug the transformer connectors back into the power driver board (without connecting any of the other boards so we don't do any extra damage just in case the power driver board is bad). You can then use the test points on that board to test the DC voltages to see if they are correct.
I would probably recommend doing this one by one in case anything is wrong you can find the problem faster.
So, for example, you could first connect only J102 and turn on the machine. If nothing starts smoking, probe for DC volts on Test Point 6 (TP6). You should have 50VDC although it could be as high as 75VDC that I've seen on mine. That's normal. While you have that test going also probe TP7 for 20VDC (should be close to 20VDC for this one) since that's also powered from J102.
If that is ok, then you can connect J101 and and check for the following:
TP8 = 18VDC
TP3 = 12VDC
TP2 = 5VDC
If those are fine, then connect J112 and check that TP1 = 12VDC. This is unregulated so it could be higher. I'm not sure on exactly what, but it might be 20VDC when you measure it.
J115 doesn't have test points and that is VAC for the GI lights, so let's skip that for now.
Let us know what you find. Hopefully we are getting close to the problem.