Need advice on new Mini-ITX build

I am building a mini-ITX gaming rig for a friend of mine based in Okinawa Japan. I will be shipping it to him with him paying shipping and handling. Hence the Mini-ITX. 

This is the current configuration I have for him. He gave me a max price of $1500 which must include a copy of Windows, a BD Drive, Wireless AC, Keyboard, and Mouse. I would like to add a Liquid cooler for the CPU but am having a hard time selecting a good one. Some say an 212 EVO would be fine but the limited clearance over the CPU from the fact the PSU is mounted above the CPU seems to point to Coolermaster intending people to use liquid cooling. I also want to improve the cooling as much as possible. I plan to add the DEMCiflex Cooler Master Elite 130 Mini-ITX Magnetic Dust / Fan Filter Set - 4 Piece kit from FrozenCPU to help keep the dust out of the case. 
Another thing I need advice on is which R9 290 to put in the case? I would prefer to have it exhaust out the back of the case but still want a ballin 290 for the money. The original idea was to go with a 770 but the 290 whoops the 770 on most everything according to Anandtech and PCPerspective as well as others.


PCPartPicker part list: http://pcpartpicker.com/p/Vfjst6
Price breakdown by merchant: http://pcpartpicker.com/p/Vfjst6/by_merchant/

CPU: Intel Core i5-4690 3.5GHz Quad-Core Processor ($214.99 @ NCIX US)


Motherboard: ASRock H97M-ITX/AC Mini ITX LGA1150 Motherboard ($88.98 @ Newegg)


Memory: Kingston HyperX 8GB (2 x 4GB) DDR3-1600 Memory ($79.99 @ Amazon)


Storage: Samsung 840 EVO 250GB 2.5" Solid State Drive ($129.99 @ NCIX US)


Storage: Seagate Barracuda 1TB 3.5" 7200RPM Internal Hard Drive ($49.99 @ Amazon)


Video Card: Sapphire Radeon R9 290 4GB Tri-X Video Card ($389.99 @ Newegg)


Case: Cooler Master Elite 130 Mini ITX Tower Case ($34.99 @ Newegg)


Power Supply: EVGA 750W 80+ Gold Certified Fully-Modular ATX Power Supply ($79.99 @ Newegg)


Optical Drive: Asus BC-12B1ST/BLK/B/AS Blu-Ray Reader, DVD/CD Writer ($43.99 @ Newegg)


Operating System: Microsoft Windows 8.1 (OEM) (64-bit) ($89.99 @ NCIX US)


Case Fan: Noctua NF-R8 redux-1800 PWM 31.4 CFM 80mm Fan ($12.99 @ NCIX US)


Keyboard: Corsair Vengeance K65 Compact Mechanical Gaming Keyboard Wired Gaming Keyboard ($89.99 @ Amazon)


Mouse: Logitech G500s Laser Gaming Mouse Wired Laser Mouse ($52.48 @ Amazon)


Total: $1358.35 
Prices include shipping, taxes, and discounts when available

I would go for the Corsair 250D as a case, which is of course more expensive but you seem to have some spare change so I do think you should take a look at it. Also, why do you want to liquid cool a non-K CPU? If you switch the CPU for a 4690K then I would go for a Corsair H100i which fits perfectly into the 250D (a shame if it wouldn't..) The H110 doesn't, though.

The 250D wont fit the R9 290. I already tried on PC Partpicker

I would need to change the R9 290 card to something less than great.

I don't think so. The only card that won't fit the 250D is the 7990. Try to go for another R9 290 design.

Take a look at the Sapphire R9 290 TriX OC. It wont fit. 250D max length is a 290mm long GPU. The Sapphire R9 290 OC is 305mm. Do the math. The 250D only fits max length of 11.4 inches. The current card is 12 inches. I dont want to sacrifice the quality of the card for a cooler case.