Yeah you can spend whatever you like really. You can get a build like that to drop under $1000 without too much drama, mainly by scaling the graphics card back to a more sensible level.
The R9 290/290X don't make a huge amount of sense right now as there aren't any non reference cards on the market and if there is a card that needs it.... I've heard rumours that they are coming in January, but it all seems like a bit of a mess. Some custom PC shops in the UK are selling R9 290s pre-flashed so they effectively become 290Xs, I'd imagine its the same more or less everywhere. They still represent pretty decent value for money, but I'm not sure I'd be encouraging anyone to buy one in the near future.
If I was buying a 280X I'd probably go for the Gigabyte GV-R928XOC-3GD as its among the cheaper and faster cards, and is very well reviewed. There's a lot of models with about $10 of that though.
Small cases are always going to be hugely limited in terms of airflow. The SG09 has it's PSU at the front where you would normally expect an intake, so it draws in air from the sides instead. It works, but I'd imagine a lot of it is blocked by graphics cards. The FT03 is an unusual concept in that all the air comes in the bottom (and bottom/side) and goes out of the top, by way of a couple of angled fans. I'd imagine it's a nightmare to build in due to the unconventional layout, but the footprint is tiny for mATX and I think it looks great.
Either case should support a basic 120mm radiator, but airflow is just as important in a liquid cooling build as it is in an air cooling one. I'd generally just stick to air coolers unless you plan to move it around a lot (then a heavy heatsink starts to become a liability).