If I obtain a the proper System 2 wiring harness or construct my own, what are the chances of destroying something? With the exception of the controls (ie joystick vs light gun) what are the chances of getting a System 2 44-pin wiring harness and have it be the wrong one?
Quite high..... I don't think that you identified the board well enough to be absolutely correct. System 16 and System 2 harnesses are actually different on a per game basis. That's to say that the games are effectively dedicated and do not follow the same wiring scheme, even though they run the same hardware OS.
Just to give you an example.... I recently picked up a complete but stripped SEGA Virtua Striker Upright manufactured in 1996.
I've spent the last few weeks putting it back together. The Main Board and the Rom Board, came with the machine as did the shield case and filter board that they live in. BUT! the manual I had, didn't match the board configuration at all. It said that there were 3 boards that should be in the case. A main board, a rom board AND a video/media board. the odd part is that the main board has got the plug in connector for the media board to go on to.
I phoned SEGA and they tell me that I should have a media board and that it'll fry the main board if it's not connected when the power is supplied!!!

So... I phoned SUZO (Happ UK) because they were SEGA dealers at the time this machine was sold. They tell me no it shouldn't have a media board, just plug it in it'll work fine.
Then I check the wiring schematic for the cab....

The loom doesn't match the manual configuration. It took me a week to trace all the connections in the cab and on the main board. Just to confirm that the loom was safe to connect.
I especially paid attention to the main board..... traced all the connections to see what they went to.
Luckily!!! the loom matched up and when I applied the power the game fired up and ran first time! NO MEDIA BOARD!! Thats how much SEGA knows about their own damned product.
The moral of the story is..... DON'T believe everything the manufacturer or the circuit diagrams or the manuals tell you and certainly don't base your identification on photographs of other boards that you yourself admit don't match.
If you want to know if it's safe to connect your loom, check the power rails on the board, and trace where they go to confirm which ones are the positive and negative. Figure out which ones are 5V and which ones are 12V. Figure out where the RGB output and sync lines feed to and figure out if all this matches your loom. The same thing applies to the audio! if the board has an on board amp, then check where the speaker lines feed to. Confirm all of this matches up with the loom BEFORE you connect the power.
If you don't, then you may not be as lucky as I was and you DO risk frying your board in one way or another. There's a lot of variation in System 16 Looms.
Best Regards,
Julian (Fozzy The Bear)