-Motherboard: MSI 760GM-P34 ($49.97) or the Asus M5A78L-M LX Plus AMD 760G ($59.97)
Do you realize that those boards are based on such old technology that they have neither SATA 6Gbs nor USB 3.0? Now, as someone else pointed out, a mechanical HDD will not even tax SATA3, but USB 3.0 might come in handy if you get an external hard drive for backups.
Secondly, think about your storage. How big is your current HDD? Could it be that you could get by with (just) a 120 GB SSD?
As for what GPU, may I recommend that you do some research into which GPU's work best, or at least have the fewest problems with those games.
The hardware requirements for FS 2004 is An 8 MB, 3-D video card, and FSX is a 32 MB DirectX 9-compatible video card.
I'd rather see you buy a good PSU and a better motherboard than a higher end GPU or even more RAM.
As for the idea of an APU, hmmmm....