Using an auto ecu on a manual gearbox swap is usually pretty straight forward with the eec-iv/v ecu's - all you typically need to change is two bytes (the 'Transmission Type' (aka TRLOAD) and 'Transmission Strategy' (aka TSTRAT) parameters).
Now, compare that to altering an ecu from a different type of engine and it's a lot more work. From a circa '97 ecu and looking at swapping the spark parameters over you'd have about 20 tables, 30 functions and numerous scalars. Then add in all the other stuff like engine displacement, injector size, MAF transfer, estimated load tables and so on you get the idea of what's involved. It can all be done but I'm not sure a tuner would tackle it as a 'mail order' tune.
Out of curiosity, what was the 'catch' code of the original ecu.