Intel Core i5 6500 - RM 824
Gigabyte B150M-D3H (D4) - RM 379
Kingston 16GB (8GB x 2) DDR4 2133MHz Value RAM - RM 290
Palit GTX1070 8GB GDDR5 Jetstream - RM 1999
Kingston SSDNow UV400 240GB SSD - RM 255
WD Blue 1TB HDD - RM 209
Superflower Leadex Silver 650W - RM 379
Tecware Alpha - RM 199

Total: RM 4538 (ETech price inclusive of GST)

Alternative build with i7 6700 + GTX1060 is also possible, but for better graphics settings (ultra), GTX1070 is more recommended even on 1080p only. Witcher 3 is not that CPU demanding, i5 can handle this game very well.
GemFive with coupon code can get 12% off but the only GTX1060 (MSI Gaming X) on GemFive is currently out of stock, RM 1284 after applying the discount.

Hmm not quite understand what you mean.

Do you mean you gonna reuse the R9 290 or sell the R9 290 and add the money into your budget?

mITX build is compact in size, meaning you are limited by future hardware extension, especially HDD/SSD expansion, no SLI/CF support, no extra PCIe slot for 3rd party PCIe expansion card (sound card/USB hub etc.), limited fan header (though can be solved by getting a fan hub), 2 RAM slots only etc.

What you get with mITX (SFF) build is portability/mobility and space saving.

Better mobo as in more features? If you mean quality then don't worry so much about Gigabyte mobo, no problem reported from forumers here so far and it is advertised as "ultra durable" somemore 

As for PSU, it is one of the best that you can get with RM 300+ budget (Seasonic M12II EVO is also a good PSU to consider within this price range), RM 450+ can get you a tier 1 Superflower Leadex Gold 650W PSU.

GTX1070 is packing with twice of the performance of R9 290, so you might need to run on med/high settings to get a stable 60+ FPS in Witcher 3 (1080p of course) with R9 290, if you are ok with this then I think it won't bother you too much.

And please let me know your exact model of R9 290 so I can choose the case appropriately (clearance issue).