I just checked, if you add this to your cart at Microcenter and a z77 (used the Asus Sabertooth to check), it brought the MB price down from $239.99 to $199.99 So I assume the $40 offer still works
You might want to try other cooler master cases such as the 922 HAF and the HAF XM if you are looking for mid tower's, 932 HAF or HAF X for full towers. I believe all of those support bigger CPU fans and such
If you got around $25 to spare and wanted to replace it if you find it to be unsatisfactory, Cooler Master Hyper 212 EVO is a cheap and effective CPU cooler. Widely used and highly rated
I remember when I was starting high school how GTS 9xxx series nvidia cards were like $300+ dollars, now you can get them for the same price as call of duty, shows how quickly video card's are advancing compared to processors, which are stagnant because they are ahead of the video card right now in terms of bottlenecking.
Do not care what people are saying about the case, it is just meant to hold in the parts which are important. That being said, it is a nice build, will do you just fine for engineering. Until I read the comment about having the external hard drive i was a little worried about storage but all in all, a good build.
You can save a little money by getting the Coolmaster 922 HAF mid tower i believe. PSU i'd go for a good 80 Plus 650 instead of 750, seems like overkill.