Areaportals don't have to fill up the thickness of the doorway, only the width.
Make them only 1 unit wide, put it on one side of the doorway. Then on the next doorway, put another 1 unit wide areaportal and position so it still fills the doorway but doesn't line up with the first areaportal. And so on.
I really enjoyed both the detailing and gameplay on this map, so if you do get the fps issues addressed, you could have a winner.
Incidently, I didn't have any fps issues at all (think I was seeing a solid 50-60 everywhere), but I play with Chris' configs for dx8 on top of having a pretty good graphics card so my feedback on that won't be particularly useful.