I'm not so sure about the finer details of the older ECUs. The newer drive by wire cars do 'limit boost' per gear, but it is done via target boost reduction and wastegate limitations by capping requested torque.
I'd recommend checking out the RomRaider forum if you haven't yet. They'll be a bit more versed in stuff like that. We do have a few members here that may have some advice for you though.
Cool project =)