So what is not working?, It sounds like the game is coming up. When a Bally game comes up it kicks out all the ball locations like the saucer and kicker in case a ball is stuck there. That's part of the boot. Afterwards the LED on the MPU flashes dimly which sounds like your B&I (that's the official name of the Weebly board) is doing. Are the displays lit up? Can you press the self-test button on the front door and put the game in test mode?

Disconnect J1, J2 and J3 on CPU board (only J4 connected) and see how many flashes you get. If you get seven, reconnect connectors one at a time to see what's causing the holdup.

Congrats on all the connector rebuilding. That's a lot of pins. I hope you drank several beers afterward.

If the MPU diag LED goes to half brightness and stays that way you have passed all seven of the MPU's power up tests. When the MPU diag LED blinks there is a delay between test flash one and test two. When you first power on the MPU the LED turns on briefly and then goes out. At that point is when you start counting flashes. After flash 7 the LED will remain dimly lit at all times for all bally/stern games except for a few exceptions like Flight 2k (not future spa).

I think it raises the drops and kicks out holes at power on so it sounds like you are actually in attraction mode but the lamps are out and the displays are out.

Start at the transformer/rectifier board. The 3/4a fuse is for the displays. Then 10a fuse is for the feature lamps. Check those fuses and see if the connectors look like they are burned up. With a DMM you can very carefully measure for the high voltage (and lamp voltages) starting at the rectifier board.

Is this a multiball game? Or better question, does the B&I board think it's a multiball game? Bally games with more than one pinball will boot and not come on line if a ball is missing. So first thing I would do is check the MPU and make sure it's set for Future Spa.

Once you confirm the B&I board is set properly for FS put the game in switch test and make sure there are no stuck switches and make sure all the ball rest spots like the outhole are registering when a ball is there.

good visual inspection of the backbox light board. They are usually two strings of bare wires going around to each lamp stapled to the wooden board. Look for any problems like crossed over wires or evidence someone in the past messing around with wiring. Its possible for the little spring thing in a center of lamp socket to break, fold over and touch the barrel creating a short. Possible a bad lamp could be shorted. I would pull all the lamps out. If you having trouble finding the short and getting desperate, break the GI into sections to narrow down where the short actually is. Someone could have wired up the J3 rect plug wrong too. Very common to see the GI wires hacked around burnt connectors.

it's pretty much been said, but you have narrowed it down to the back box which is J3 on the rectifier board.
the general illumination is AC so there isn't anything on the rectifier board to go wrong.
the AC comes from the transformer, one line through the 20A fuse to pins 10 & 11 on J3, that you already know, and the other the return being ground, pins 1 & 2.

with all GI bulbs removed from the backbox, and J3 unplugged from the rec board, check for continuity between 10 & 11, the orange and red wires which should be soldered together to one of the GI braided wires and pins 1 & 2, the white and green wires, also soldered together to the other braided wire.
you don't need to check at the pins, you can just check where you see the orange/red and green/white wires on the backbox door.

if no continuity then great! something to do with a globe itself or possibly when the globe is seated?
with the game on and J3 connected on the rec board start reseating the globes and if the first one causes the fuse to blow it's really lucky you happened to pick maybe the faulty globe or there is an issue further back. Try another globe in a different holder.

if you have continuity, causing the fuse to go open, it is likely to be, the orange/red and green white soldered incorrectly (mixed up), a shorted/damaged globe/globe holder, a soldering hack, an oddity like a screw from the front shorting through the door or something else?
so the task begins of searching for the culprit/s.

as you may already know:

J1 on the rectifier board is for your playfield.

J2 on the rectifier board id for your cabinet.

J3 is for you backbox.

F1 is for your switched lights & F5 is for your general lights

if both fuses are going open it sounds like a short to ground, but unusual for both to go open.

and it sounds like it's happening due to problem in the backbox.

i'd check your switched wires aren't joined to your general wires. you need to find where the 2 'join'. then where the 'short' is.

i had an issue where the GI fuse went open on powering up.....going nuts trying to work it out, no obvious clues, turns out it was a backbox hinge screw that was shorting to a GI globe housing.
see the hinge is touching the ground plane, and a longer than normal screw was put in shorting the ground plane to the GI.

you need to isolate everything and start from the rec board IMO

for F1 20A fuse going open:

with the machine turned OFF and with J1 & J3 unplugged from the rectifier board,

and all switched globes removed from the backbox, do you have continuity from J3 pin 6 (switched illumination bus) to ground?

That green wire is not factory.

Like they always say, stupid people do stupid things

That green wire shorted the GI bus to the switched bus. No wonder the fuses were blowing.

I'm guessing that at some point the CPU controlled lights behind the 'Future Spa' stopped working, so someone jumpered it to GI so that it was always on. Might've run that way for years until you fixed the original issue the correct way, thereby creating a short.