Hi,
I put my rig together a few days ago in a HAF-X. It's a great case with loads of room so mostly you will have no problems. The areas that caused my Homer Simpson D'oh! momemts were:-
a) I too replaced the side and rear fans. These didn't come with any kind of screw thread. You'll have to create your own with the screws supplied before you attempt to screw them to the case.
b ) If you put the old side fan up in the front roof (it fits) take care to orient it the right way to allow the front panel cables to come down througth a hole in the roof. Even so I couldn't fit the roof back on with the blue USB3 cables connected, so off they came.
c) The front panel USB3 connectors are connected internally to very long cables which are intended to come out the rear of the case and fit into external USB3 connectors i.e. not motherboard headers. Rather naff in my view, but m/b headers are not standardised yet.
d) If you want the side fan controlled by a fan controller in one of the front 5 1/2" bays, you'll probably want an extension fan cable to reach from controller cable to fan cable. 60cm did for me which I anchored through bottom of drive bay area from back towards the front.
e) You can remove any HDD bays you're not occupying for improved air flow.
f) The supplied extras include an extension 8 pin power connector which you will probably need as the case is so high. I actually bought a fancy white braided extension cable, but you can't see it through the top window so the cheapo one would have done.
g) If you are fitting the ever popular Noctua D14 cpu cooler this will dominate the upper window. There is nothing else to see.
h) Without extra internal lighting the side window looks rather dark. I'll be fitting cold cathodes soon to illuminate my black motherboard against the black case. Err......
i) You get a small bag of loads more screws and risers than you will need. This is handy since I did notice with the risers that they did not have uniform threads so often had to try another.
j) The expansion card brackets are held in place by chunky thumb screws which come out easy enough but don't go back in so easily and don't provide any useful securing pressure that I could see. Worry not. There are plenty of small flat headed screws in the supplied screw bag which are far better and do the job great. Use these instead.
k) Most front panel connectors probably connect at the bottom of your motherboard (USB, firewire, power on etc) You might want to give some thought to the sound connector before you put the motherboard in. I found it really fiddly connecting the HD sound connector between the case side and the cpu cooler when already installed.
l) You'll probably want to fit the cpu cooler on the motherboard before this goes in the case. The rear cpu cut-out on the motherboard is not big enough for a noctua support on a UD7 (and a few other boards).
On the whole there really aren't any issues, but that might save you a few minutes.
ATB