I've not yet seen any pre OBD2 ECUs that are easily reprogrammed, none that can be done down the diagnostic link. Some of the later 8V ECUs have EPROM and it may be possible to modify others using a daughterboard with EEPROM fitted. I don't know which ECU you have, I have been looking at the early 16V but haven't yet managed to pull the code.
I would recommend a USB interface using the FTDI chip, that way you will not be going through the UART which remnmoves any possible problems with the baud rate.
The code that I am modifying was originally written to communicate with my own ECU design, I have used an interface to convert the protocol to the Suzuki protocol and have logged data succesfully, I just need to modify the software to work directly with the Suzuki protocol. I have helped a few other guys that have tried the protocol with an ALDL interface and it is working with an Escudo in Russia, a Tracker in the US, a Baleno in India and my own Vit here in the UK so it seems pretty universal.