Wow... you just opened up a whole can of worms. One of the most annoying things about these cars is that the ECU pinouts differ from year to year. If you don't have the exact ECU for your car, you'll need to make a good plan-of-attack and solder each wire on the new ECU's harness to the corresponding wire on the old harness. Thankfully, the color coding didn't change much throughout the years, so it shouldn't be too bad.

As for whether or not you can run MSnS through your stock harness... yes and no. MS units aren't designed to withstand engine bay conditions. The heat, but more importantly, the moisture will affect it. You might be able to get away with filling the case with a potting material, but then you'd lose the ability to modify the board in the future.

Also, you would need to be fully prepared to run the unit as a complete standalone, which most people aren't ready to do. This means finding new power sources for all the sensors that require VREFs, controlling the alternator's voltage output, wiring various sensors to the dash, and controlling various auxillary systems (fans, A/C, etc.).

-http://www.symtechlabs.com/-