Cheapest FPGA PCIe board for Software Acceleration
You could look around for an old ML506 or ML507 from Xilinx, but really $1300 is a reasonable price for these boards.

There is one other option I can think of: the Raggedstone 2 from Enterpoint, at prices from about $400 upwards according to the FPGA (Spartan-6, different sizes). They have a range of other options with up to 25 FPGAs, but probably outside your price range