What kind of I/O do you have on the Allen Bradley unit ? USB? Ethernet? RS-232? RS-485? Just plain vanilla analog or digital?
If you've got a RS-232 port and also have software that's sending Yaesu-version GS-232 commands, the commands you can expect to need to intercept are in here:http://www.g6lvb.com/gs232a.pdf
If you can configure your unit to catch those commands, you're good to go... but I don't really know what your controller is capable of (seems like it could be anything depending on add on units).
Making the unit pretend it's the Yaesu control box is probably the way to go.