My first suggestion would be to try and collaborate with a university. Some universities have a clean room and manufacturing equipment for prototypes or research. If you could find a professor or grad student who was interested in your project, you might get everything you need.
Another option is a prototype foundry like MOSIS.
The university I went to would use this service to fabricate the designs for their graduate level semiconductor courses. I am not sure how custom your design could be using MOSIS though because you typically share a wafer with other orders to reduce cost.