I did similar modifications as Mike to give my self two independent systems (switch in between for emissions testing). I ran the alternator off of a voltage regulator from a Dodge Omni. That worked fine, but I had to buy a couple brands before I found one that offered stable regulation. I put a board in the upper case of the MSII to house a 5V regulator and 9V regulator to run sensors. MSII ran fuel, ignition, and IAC. Near the end, I had a circuit to raise idle RPM before engaging the A/C compressor. If you want to completely remove the stock ECU, you should look through the electrical diagrams for the MFI system and find a way to supply all of the outputs provided by the stock ECU. Otherwise, you'll probably miss something and waste time diagnosing a mysterious condition.

Corbin
'97 GSX dressed like a '95 ESi