Howdy! Other things you should probably consider are whether the FPGA you choose supports the complexity of your design (e.g.: number of gates, memory access, custom IP, etc.), the availability, and how easy it is to develop for and program (as this can add both $$$ and aggravation to the cost of the chip itself, which I'm assuming you've already considered). If you need multiple clocks and they run at frequencies that are not multiples of each other, you will also need an FPGA capable of supporting them. Some FPGAs have 5V-tolerant IOs, which might save you having to deal with level shifting.
My suggestion would be to start by spelling out all your requirements, and identifying those things you don't yet know (e.g.: how many gates you will need, or whether you will need any kind of custom IP), and then look for a possible candidate by doing a parametric search at one of the large distributors. Rather than going directly to building a custom PCB, I would start by buying an evaluation board (the availability of which could also well be one of your req's) and use that as a starting point. The good news is that, as long as you don't use any custom IP, the code tends to be pretty portable, so it's probably not the end of the world if your choice ends up being incorrect for one reason or another.
IMO, breaking things down into multiple FPGAs is risky. It can be done, and it's probably easier if you isolate whole functions, but it will likely also increase cost and complexity.
Oh—and don't forget to look for existing solutions you can borrow from. There are lots of emulators out there, so someone may have already solved your problem, at least in part.
—CC