How can I get touchscreen (HID) data into Windows 7?
If you're using the FPGA just for the PCIe I would choose a different route. You mention USB HID, and I think this is the best way to get the touch screen data in your Windows (or any other OS) computer. While I don't think multi-touch is possible with a common HID driver like a mouse driver it should work for single-touch.
There are plenty of microcontrollers which have a USB device stack built-in. NXP lists a few dozen of them, the LPC1342 being a low level device. For the rest you only need an ADC to read your touch screen, so the LPC1342 should do.