Hello Nate
You will be able to correct the machine denomination when you get your keychip. The machine has to have zero credits to key it, that's easy to overlook sometimes.
Unfortunately you can't upgrade a 13" cabinet to be compatible with the 044 MPU. The 044 MPU has different backplane connectors and IGT apparently never made a 044 motherboard that will fit in the older 13" cabinets. You can however upgrade to a 3902 MPU which will allow you to play SIMM based I-game and Game King software on it. That is just a straight MPU swap from the 3802 to 3902.
The board tray with connectors plugged into it above the MPU tray is your input/output (I/O) card tray. That's where switch inputs, lamp outputs, and other I/O signals are processed.
If you really want a machine to play 044 games on your best bet is to buy a 17" machine that has already been upgraded with a 044 MPU and motherboard in my opinion.