Look, Kellys_eyes, if you don't want to help, that's ok.
Honestly pal, chum, cobber, fella, I'm not actually against what you're trying to do. We all have a vested interest in knowing how things work and would be more than eager to accommodate your needs but regardless of the pictures you might get to post the end result will remain the same. The whole unit is a 'computer' with the control program stored in the EPROMs. The program will require to be 'disassembled' to identify the areas that do the actual 'control' if you want to modify any parts of it. The hardware part of it is 'fixed' - other than maybe boosting the port current handling capabilities you can't really add to them.
We might identify some of the input/output ports on the main connector - you can do that from the vehicle schematic anyway - and re-programming is usually possible via the CANBUS protocol and the ODBII connector in the vehicle itself.
There may be some documentation on the EPROM contents
somewhere but it's usually 'unpublished' and the manufacturers certainly won't be helpful.
Even those that HAVE managed to decode the content are likely to keep such information to themselves for the 'value' it has - re-programmed EPROMs are not cheap..... possibly the reason for your current course of action?
Either way you will need the software to disassemble the EPROM contents and knowledge of assembly language to make changes. This will require identifying the main processor type - a clear picture of the board helps here.
Have you sourced any solutions to dissolve the silicon gunge? Acetone perhaps? That's probably the only way to get a clear enough image of the board and the parts we need to see.
You'll also have to desolder the shielding over the section of board that houses the processor itself.
There are open-source vehicle ECM units but I don't know if there's one specifically adapted for the Jeep - these would be the best route to go if you wanted to make your own ECM that would be fully programmable to specifications YOU want.
By all means clean up the board and allow us a closer look - seriously, I'm curious to what's in one as much as you are.
As mentioned by
@davenn the Jeep Forum is a useful place to go for information - a quick Google found this article on repairing dud ECM's (capacitor changing) here:
http://www.jeepforum.com/forum/f12/crash-course-brain-surgery-replacing-capacitors-ecu-492597/
and there's bound to be more such information - or someone there with more intimate knowledge of them.