Success ! I just received the diode pack I needed to fix my FPGA board from Digi-Key (Really impressed with their international shipping) and made the repair. SOT−323 packages are hard to solder even under a microscope, but fortunately I only had to replace one.
The drive works great with the correction that you mentioned Mariss so thank you for that - I'll publish the fix to the H-Bridge designs incase anyone decides to use them. The motor's a little noisey but I'm going to put that down to the wires I have running all over the place, there's probably quite a lot of noise on all of the signals. Now I can have a play with the Verilog code and carry on experimenting.
Update: New board design completed, complete with improved track isolation: https://oshpark.com/shared_projects/NTc0L6wF / H-BRIDGE | Projects | CircuitMaker