My 91 Civic Si is generally great but after driving if I park and go to restart the car will start right away but then stall. If I hold the gas pedal down a bit and keep the revs up it will eventually recover and I can drive normally. I replaced the main relay but it had no effect. What could it be?

Did you replace it with a new (packed from the factory) or another used Main Relay? If it was a used relay - it might have had the same problem as your original relay. Get your old relay (if you have it), and check this page - http://www.markl.f9.co.uk/howto/electrical/main-relay/main-relay.htm

You will find info on how to check for "dry joints" on your relay. If you find any dry joints - most likely your other relay has the same problem. If it's not that, it would most likely be the Igniter Unit. Search for a thread titled "Sparkless & In The Snow" in this forum, and you'll find information on how to check if your igniter is good or not. If it's faulty - replace it.

When did you change spark plugs, spark plug wires, distributor cap and rotor?