I did this exact mod - but flipped the heatsink to be CPU side, allowing the fan (nff12) to pull fresh air from the GPU vent.
Having the fan on the GPU side also allowed for a larger GPU, a Zotac 1070 mini.
The warm air pooling in the CPU chamber is dealt with okay by passive exhaust.
I get idle temps on my i5 4590 of about 30 degrees C at 20% fan.
Full load, at 50% fan (1500rpm), it gets to about 50 degrees C.
P.s. be careful where you cut, I managed to keep both 2.5" bays - I've seen a couple people lose one.