Intel Core i5 4460 - RM 805
Asus H81M-K - RM 240
Kingston HyperX Fury 8GB DDR3 1600MHz RAM - RM 179
Zotac GTX960 2GB GDDR5 ZT-90310-10M - RM 799
WD Blue 1TB HDD - RM 215
FSP Hexa+ 550W - RM 189
Bitfenix NOVA - RM 149
Total - 2576 (Techview price inclusive GST)

Your current casing is ATX form factor, or at least mATX? (Just have to make sure it can fit the mobo)

Intel Core i5 6400 - RM 809
MSI H110M Pro-VH - RM 329
Corsair 8GB DDR4 2133MHz Value RAM - RM 200
Zotac GTX960 2GB GDDR5 ZT-90310-10M - RM 799
WD Blue 1TB HDD - RM 215
FSP Hexa+ 550W - RM 189

Total: RM 2541 (Techview price inclusive GST)

Latest Skylake i5 is same price as Haswell i5, the problem is the mobo which can support DDR4 is expensive, the lowest end chipset (H110) with DDR4 support is going to cost you RM 329, which is significantly more expensive than DDR3 based mobo.

It is the lowest end chipset, you can top up RM 70 for MSI B150 Bazooka D4 to get 2 extra RAM slots and more SATA ports.

R9 390X for extra RM 300? RM 1099? Or you mean R9 380X?

Which MSI Gaming M3? B150 one?

Yep, AMD card requires more power compared to same tier's Nvidia card, so if you want to get AMD card, you are advised to top up some money for better PSU.

The difference between B150 and H170 isn't huge, H170 can support up to 8 USB 3.0 ports (support still based on manufacturer though) and RAID support etc. You can just get B150 chipset mobo if you are not going to use the features offered by H170, B150 is slightly cheaper than H170 in overall.

Learning needs time so no worries, take your time 

An i5 can hardly bottleneck a GTX970 but it still has to depend on what games you play, those CPU demanding games will likely to hit max usage on all cores.

i5 6400 is 0.5GHz slower than i5 6500 (base clock), you can consider to upgrade to i5 6500 for slightly better base clock performance.

For me, the slightly faster/slower base clock don't take much effect. But it's up to you to choose which model you wtb.

are you mean the 970 is RM600 expensive than 960?

I think if you can afford 970, I don't see the reason why you go for 960. Take some time for survey the benchmark between both and you will get the answer.

You can use it but the board will throttle down the RAM to its highest supported frequency, 2133 Mhz.

Keyboard?!?! 

Only Z series mobo supports > 2133MHz for DDR4.

You can look for Kingston HyperX Fury series RAM, just around RM 30 - RM 50 more expensive than value RAM, much cheaper than getting a Z series mobo.

Not necessary if not heavy multitasking or doing rendering work.

I think you can get the 8gb hyperx fury ram for about rm188 on lazada. Saw it at that price few days ago.

Due to out in Q1/Q2 2016. Life cycle is different for each series because there is no fixed timeline on how Nvidia rolls out new series.

Pascal and HBM2