Do you still have your .edu email Perf? If so you can get Win 7 for 30$ (well, potentially)
For the fans, I doubt you will need 2 intake fans. Depending on the cpu cooler you choose and where it gets it's air from you can move the fan around. If the cpu cooler draws air from the front, you'll want to move the side fan to the front, if it draws from the side, you will want to leave it as is.
The CPU is going to be the hottest running part in the HTPC especially since you arent using a dedicated GPU (yet)
Also, most of the cpu's you linked to do come with fans.
http://www.newegg.com/Product/Product.aspx?Item=N82E16819103687 -- Look under specifications. It says Heatsink and Fan included.
After looking up the stock cooler, I can say that it should work just fine as long as there's a second fan directing some air at it. That side fan in the case should work just fine for that. This will hopefully keep the cpu fan from spinning up, keeping noise down. In other words, Id actually hold off on the aftermarket cpu cooler for now. You can always add one later.
Other than that, I dont have anything to add at the moment. Im sure you'll be fine with the building part, considering your line of work.