Fascinating. I also started with some work on duke3d, based on a merged version of my amiga port back from 2003 and the last update from icculus. at least i don't have any endian issues, because i had removed them already back in 2003.... was the most work, took me weeks as far i remember.
netherless, wish you all the best for your port, and if your port is really playable on AGA, than i can stop working on it...