First thing to look would be if any of the sockets for the bulbs are touching any switch or wires. It's possible when you installed a LED you accidentally shorted the socket to a switch..

Do you have a multimeter ? Set it to continuity and test :

Verify you can measure the short yourself by checking :

-With the connectors plugged in , check for continuity between J209 pin 4 and J207 pins 2 through 9. Do you read a short ?

-Between J209 pin 4 and any ground plane , do you read a short ?

Verifying the short is on the board itself :

-Unplug both connectors and to the test directly J209 pin 4 and J207 pins 2 through 9 on the headers on the board. Do you read shorts ?

-Connectors unplugged and J209 pin 4 and any ground plane. Do you read a short ?

If you have a short here , it means there is a short on the board.

Verify if the short is on the playfield :

-Do the same test on the connector housings of J209 pin 4 and J207 pins 2 through 9 while disconnected. Do you read a short ?

Last , measure between J209 pin 4 and any ground plane while J209 is disconnected , do you read a short?

If you read a short here, there is a short on the playfield switches somewhere.

It is not impossible there is a short on both the board and the playfield. While in switch test mode , if you pull both J207 and J209 , does the test still show the row shorted ? If so , definitely the board has a short , and u18, D6 , R57 and R58 could all be the culprit.

-During all of this , you did measure that your +12V is solid ? A low 12v can very much cause such interpretation of a full row "closed" or shorted.

-Can you provide a picture of the CPU board connections with J207/J209 and the resistors and ICs just above ? This also could be a case of battery acid
corrosion on the board.

Wiggling connectors on the machine should never make things turn on and off like your switches error , so there seems to be a bad connection there , maybe corrosion once again, and headers and connector housings should be changed.

That fuse holder should not be burning up and should be replaced ASAP. Verify its the good size fuse in there as well. This powers the GI (general illumination), and these lamps are on all the time. After seeing damage like this , it's worth checking all fuse holders and pin headers to make sure everything is in order. This 30 year old machine might need a bit of love if you plan on running it another 30 years.