Glad ya got some help here

Are you capable/do you feel comfortable building it yourself? If you DIY you will be able to get a much better machine than pre-fab. Kinda assuming you can DIY since you started off looking at individual parts instead of a pre-fab.
I would buy the parts whenever the deal is best unless you have a deadline of when you want the computer finished. If there's no rush then buy them when you find a good sale for that particular item.
For cases, you need good airflow and room for cables as Cliff mentioned and also make sure your Mobo is compatible with it. Most are fairly universal but sometimes you find a case or board that has the holes in odd places. Rosewill makes some good cases.
I would highly suggest a
minimum of 8gb of RAM. Your current Mobo choice says it has 4 slots so you could easily put 16gb in there if you can find it for a decent price(check Newegg.com). RAM is one of those things that is fairly cheap to increase but you'll kick yourself if you don't have enough. All Windows OS's that I've worked on are RAM hogs and require a few gigs just by themselves(Win7 takes ~20gig of storage, easy to see how it requires a few gig of RAM). Then when you figure a high end game requires 2 gig and you want at least 1-2 gig free for your browser/music/other stuff you're doing. If you figure 2gig for Win7 and 2 for your game, 4 is only just getting by, 8 or 16 would run better and allow you to do other stuff.
For the CPU I would also highly suggest a multi-core, either a triple or quad. I have a triple and only ever max when rendering HD video(although as I type this while playing RS HTML5 Beta my CPU is going between 60-80%, no other game does that, oddly).
I'm not sure the difference in Graphics cards, but 1gig of RAM on your Graphics card is helpful because that is that much less of the system RAM used.
Question: What are you doing with/what is happening to your old one? Can you use the screen from it(thus saving ~100$)?