Your alternator may be back feeding your ignition system. More info would be helpful as to what electrical modifications have been done. Sometime a diode is required in the alternator feed line. If you search for diode on here you should get the information you need. You can prove this issue by disconnecting the alternator and start and shut down the car and see if it shuts off.
is there a electric fan hooked up to the ignition switch, if it is it could be back feeding the electrical system, I have seen this happen a few times when you turn the car off the fan become a generator and some times they'll run for afew minuites.
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