Good Luck on your situation !! I know it has to be stressful.
Car-Part.com--Used Auto Parts Market
is my preferred on line used parts "tool".
Sorry - I don't know about ins and outs of replacing Honda ECU's. If its true that it has to be reset by a dealer you might have to fork over the big bucks anyway.
But you certainly can ask at honda-tech.com. In my opinion an account on that site is worth having. There's a lot of good detailed Honda info to be had from their FAQ's, and also by asking your question(s) on the message board. Use the board for your generation Civic:
Honda Civic/Del Sol (1992 - 2000) - Honda-Tech