Good looking build, except he wants mATX. I agree the CM 690 is an exceptional case for the price, but its a full sized tower, hardly portable.
If it's portability he's looking for, why not go for a laptop? A mATX case may be lighter and less bulky than a standard ATX case, but you're still packing around a desktop which is a pain in the a$$.
The other issue one runs into with mATX cases is cooling. The OP said "ADDITIONAL COMMENTS: I would like it to not be loud. Lots of multitasking on this and be able to run games on highest settings. Maybe also an extra fan/water cooling system". Games at the highest settings means a high end video card, which doesn't mix well with a mATX case.
He is going to run into cooling issues if he goes that route, unless a liquid cooling system is in place. This makes even your mATX build hard to achieve.
Another alternative is to start with this month's $600 SBM build, but use a Q9400 and maybe improve the video card.
Or, use the $1250 SBM machine, but use only one GPU to bring the price to within budget.