After pretty thoroughly exploring the issue, I've come to the conclusion that, at the moment, CHDK and Endless Memory are mutually exclusive.
Endless Memory requires a FAT32 partition, and CHDK requires a FAT16 boot partition. folks with big cards have got around this by creating a 16gb boot partition and a 32 gb data partition and swapping them on the camera at boot with CHDK, but then the Eye-Fi card gets confused and can't find the photos to upload (I think it's looking on the boot partition).
As far as I can tell, only two things will solve this - one is to enable Endless Memory on FAT16, and the other is to enable CHDK to boot on FAT32.
I've posted to the engineers at Eye-Fi, and I can bring a working setup to them (I'm a few miles away), but I want to try to find a resolution from the CHDK community too, since folks here are so amazing.
I have a working Eye-Fi timelapse system (minus endless memory): Canon SX30 + CHDK + 4GB Eye-Fi Connect X2 + Verizon mifi 2200 router. If I can get the endless memory feature to work, we'll have around ten cameras in the woods looking at a river evolve during a dam removal project and uploading the images via cell network to a webserver, which will also compile video.
That would be really cool.