>I know that the I-PAC and J-PAC use an encoder that prevents key >ghosting but a potential problem I see is that the default mame >assignments use "special" keys like shift, ctrl, and alt. I think these >keys should probably be avoided.
Interesting question. I think MAME currently has Alt combinations (Like Alt-Enter, Alt-Space) disabled, but not sure when this was added.
>Since I have to reprogram the I-PAC, I was thinking that maybe I >should take the opportunity to reprogram the J-PAC as well to avoid >some of the "special" keys mentioned above.
You'll need to re-program at some point, because the I-PAC default for P2 buttons 5-8 are the MAME defauts for P3 joystick.
>Am I going to have enough keys left over after I reserve start 1-4, >coin 1-4, and all the MAME fuction keys?
Depends what you mean by "ALL" the MAME function keys. MAME uses F2-F12 for some functions, P (Pause), Esc, Tab, Tilde, T (Tilt), 9, 0, -, =, PgUp, PgDown, and some more obscure ones. If you include all of these, you probably won't have enough inputs.