For the modifier keys - I'm hoping I'm not being dense here, but in MAME, I'm not using either SHIFT, CTRL, or ALT.
On the Ipac, I have gone through and disabled the SHIFT function, that caused me a lot of grief originally.
The main thing now is the backslash - which I'm just not using now. That apparently kicks off a 3dfx debugger, and I can't figure out how to disable that function, so the backslash is off limits.
The 3 player left/right are still a bit of an issue. When mapped to J or L, I get odd behaviors on NFL Blitz where part of the screen flickers. I'll post some more detail later, I just haven't had a chance to isolate each behavior. It's a bit maddening.
So on the modifiers - am I being dense, or is this what you're referring to? The Shift, CTRL, ALT, and Ipac shift? I think I've explicitly set everything else.