I have a same casing and modding is indeed very hard due to space.
For problem 1, what are you trying to achieve?Radiator mount? Please note that the PSU is just underneath it with very little spacing between
For problem 2, you can mount fans but size/depth is a problem unless you mount the fans externally. I have 1 fans using 15mm thickness mounted at the back to cool to CPU area but spacing super tight. on the other side you can cut the upper part for see through effect and maintain the lower half(holes) to allow your GC to draw cool air through the vent.
for problem 3, respray can be done but i recommend a pro fellow to do it (to achieve beautiful and even finish).

Other problem. The heatsink. Make sure you get a right heatsink+fan combo. Majority of heatsink+ fan are taller than 80mm

Other than that , this is a good solid casing and loving that compact look.