You may want to consider having the boards checked out before replacing them. Replacement boards have been produced, but they aren't always that easy to find. Your original boards may have years of life left in them after getting refurbished by a good tech. I had my boards repaired nearly 15 years ago and have had surprisingly few problems since. If you consider going the repair route, a couple well-known repair guys:
Chris Hibler https://pinside.com/pinball/community/pinsiders/chrishibler/contact
Clive/Coin-Op Cauldron: http://www.coinopcauldron.com/
If you're interested, Clay's Williams system 3-7 guide had written this specifically about reversing those connectors on a Black Knight pinball machine:
Oops! I Mis-Connected the Plugs and Turned the Game On!
If the plugs were cross-connected, and the game turned on, there are some likely things that could happen (this example is Black Knight; what blows exactly can be game specific, and may also depend on how long the game was powered on). First the obviously broken stuff was:
General Illumination lights.
Score displays unlit.
Flippers permanently energized and stuck on.
Drop target reset coil energized and stuck on.
Sound board wouldn't even do self test.
In this Black Knight example, here's what fried, and what survived:
Power supply board was OK.
Sound board Amp IC blown (flipper was being energized through this IC).
CPU board needed IC7 (7404) and IC5 (7402) replaced, as these were shorting +5V and ground through them (these are connected to the memory protect circuit and diagnostic switches). It also needed IC12 (7408) replaced to get the CMOS RAM working again (until this was replaced, the game always came up in test mode).
Driver board needed IC17 (7406) replaced to fix a bunch of switches that wouldn't read. Also needed IC11 (6821 PIA) replaced to fix some row inputs that were stuck "on" (surprisingly, the 4049's CMOS chips survived)