Dang Coin-In Jam error

[Dirtee]

1st time posting here, but I have spent a ton of time reviewing other posts in hopes of resolving my issue.  I've learned a lot, but I am still a newbie here and will do my best to get the terminology correct.  I'm looking for some assistance in resolving my "coin-in jam" error.  I will be as detailed as I can, so let me know if you have any questions or suggestions.
I bought a used IGT S2000 "red white and blue" machine that was non-functioning when I bought it - as such, I have never seen it operate.  Its the first machine I've purchased, so purchasing a non-functioning machine is probably not the brightest idea I've had.  The machine has a 502 mpu and I removed the varta battery.  The battery had some corrosion on the terminals, but the board itself looks great.  The other battery has been replaced by somebody (zeno energy 3.6v lithium) and is setting at 3.25 volts or so.  It is a ticket machine with the coin handling removed.  The guy I purchased it from said it was working until one day something happened. 

I have a "coin-in jam" error and neither the button lights (5 button machine) or the credits display (5-5-2) are illuminated.  I can push the little re-set button on the mpu or turn the jackpot key and get to the "accounting" menu, however I can not select any functions with the buttons as it seems they are not functioning.
I have purchased and replaced both I/O boards (14930200 & 14928001) as well as the 5-5-2 board with used "tested functioning" versions from e-bay and still have the error. 

Here's some interesting stuff: 
1) It has the coin comparitor jumper plug installed, however it is wired differently than what has been posted on this site.  Pin 7 jumps to pin 1, however pin 6 jumps to pin 2.  And yes, I have changed it so that both pin 7 and pin 6 jump to pin 1, however there is no difference.2) There are two wires (yellow and black) that have been cut and just hanging near the coin box.  On the other end there are two spade terminals and they were laying near the door cherry switch.  I have reason to believe that the door optics have been bypassed and I suspect this was part of that effort.  There are only 2 wires on the cherry switch and the work light is activated by the switch.  Also, I have no door open errors.3) I have unplugged and re-seated many many connections more times than I care to admit here.  However one time I re-seated the power supply and the machine acted like it was going to boot correctly.  For a moment I saw "play 2 coins" on the display before the error popped back up.  Since then I have tried re-seating the power supply with no such luck.
I certainly don't have a wiring diagram or an understanding of what wires should and should not have voltage, etc. but I am able to plug around at the connection to the 5-5-2 board and see there is 12v at a couple of the pins.  I don't see any compromised wiring anywhere, so I'm starting to think MPU board.  I'd like your guys input on this one - or possible other things to test.
Also, I don't have a key/ram/clear set for this machine, consequently I have not performed such a function.  What I am reading here on this site is that if there is a problem with the machine that a ram clear will likely not resolve it.  Obviously if I replace the MPU I will have to perform a clear & key, so I am looking to find which chips I need for this 502 board.  AND, does anyone recommend going to a 504 board in lieu of the 502. 

Thats about all I can think of at the moment - let me know your thoughts and questions and I will do my best to answer.  Keep in mind I'm not real savvy yet, so keep your acronyms to a minimum.  Thank you in advance for all your responses. 

[RB]

 

504B MPU recommended if you do indeed replace it. More user friendly for enhanced sound. Pictures of  the cut hanging wires would help. The 3.6V lithium isn't correct but that's not causing your issue. PM sent on the clear/key chips.

[Dirtee]

Ok - here's a pic of the loose yellow and black wires.  The cut end was just hanging in the cabinet.  The ends with the spade connectors were laying (unconnected) just behind the door cherry switch.  Thanks

[RB]

Yeah those are not important. They went to the casino watchdog system that alerts them that the door was opened.

[Dirtee]

Update:  Replaced the MPU - the unit works now.  Thanks