I've tried to get the PCI cards running, so far with no success. When I asked on the Stack, Krzysztof pointed me in a new direction:

I will try to use a microcontroller from the microchip dsPIC33 family for acquisition with a small RAM chip for storage.

These devices offer fast ADCs and are fast enough to add some signal processing.

I will then interface multiple ADC-controller with a host controller or my computer, this connection can be slow as data is stored in RAM.

With this new concept I'll soon start working on a prototype ADC board.