For now it is a one off part. If I ever wanted to make more, I'd get a professional to design it properly
At this stage it is a prototype/RnD device, so budget isn't really a concern. $100 would be completely fine.
Regarding making boards I often design and build my own boards for projects even though it would be far cheaper to use dev boards because in the process I have learnt a ton.
I plan for this to be a learning project as much as anything, so constraints are fairly flexible.
Regarding clock, I can provide the same clock that I will clock the microcrontroller from. I presume I can PLL it up to the desired frequency inside the FPGA.