I'm not sure how the n/a is wired but I believe the hot on the coil is a part of the chassis wirign and you cna keep it to power your coil, the negetive I believe goes to the stock ecu as well and the tach, if it doesn't go into the engine harness then I suppose it just feeds the tach and you cna leave it in place, as for powering your MS, first and formost wire up your hot power, to the battery , then take your switched power form wherever you like, it's realy just a trigger signal to turn the unit on
your stock fuelpump relay should still work you'll just need to pull the trigger wire out and run the ms fuelpump trigger wire to the trigger side of the relay