Doing a bit of further debugging of AGROS on my lunch break... turns out there were a couple more problems related to the restructuring, and a problem with the architecture definition for the configuration program.
Those being fixed, I now have a sample program happily ticking away with four tasks running (main, monitor, poll manager, and idle). The lights blink, messages come out on the console port, and I can type in monitor commands and have them run. Currently compiled for ARM using gcc 4.2.2 (which didn't work with the old structure), and there's no manual futzing around to get the right version of libgcc.
Maybe I'll try compiling for thumb later (now that I've got it back to a working state, so anything that breaks can be safely blamed on thumb mode).
For now, though, it's time to get back to real work.