That's a nice build you got there. To answer your questions
Intel Pro PT NICS are awesome but I would personally suggest not buying more ports than you physically need since unused ports occupy system addressing and memory resources and remain IDLE. Additionally, if not needed, I would disable the onboard LAN since it as well as other onboard devices are CPU controlled. NIC cards like the Pro PT cards incorporate their own controllers which provide better performance.
Also I wouldn't worry about naming since pfsense will do this automatically and unless changed during setup will assign em0 and em1 to pcie 1 and pcie 2 in that order if NIC cards are put into them. The caviat is that if you don't put a card into pcie 1 but put a card into pcie 2, the card in pcie 2 will be named em0.
2 Side suggestions I would make is consider potential reuse of the parts if you upgraded the router and choosing a board that is upgradable for reusability with things like and upgradeable CPU and dual channel memory would be great features for a desktop. External power is also a great consideration since, internal PSU's generate heat and inside small cases for this purposes, heat is often trapped inside due lack of good ventilation. So, based on my suggestion above I chose the Intel DQ77KB for my new build.
Im going to supply a link here that illustrates a thin mini-itx board that is externally powered. Personally its a good choice but you buy what you like. Again, just showing you something with external power that is value priced and gives you upgradability.
http://www.amazon.com/Intel-BLKDH61AG-Thin-Motherboard-DH61AG/dp/B00G9EXYLS/ref=sr_1_1?ie=UTF8&qid=1459610896&sr=8-1&keywords=thin+mini-itx
If you end up going with a externally powered board, two considerations apply since they use what is basically a laptop charger as a power source. 1st consideration is buying one that supply the required power needed by the board. 2nd is ensuring that the plug that goes into the motherboard is the same inner and outer diameter needed by the motherboard. These are easy to check on and are a must to do since there are so many of these types of chargers on the market.
