I haven't looked at the MegaSquirt in ages but can't you use an output and have it activate on a number of conditions logically OR'd together?

Yes, but I'm using a diypnp, which has a very limited number of I/O options.. I'm already using almost every one ( running sequential injection as well).

Using this micro controler will let you pull data from the serial port to trigger, so any data available to the logger would work... You could possibly use it to pass a fake obdii signal with s fair amount of work.. ( maybe)