Pixhawk platform is open source (hardware and software), hence the clones, which in many cases (not all) are equally as good as the 3dr original version - for under half the price! I built an F450 also just over the last month (my first multirotor build) using Pixhawk clone also. I have experienced a few issues but then I have also seen reports of these same issues affecting 3dr version (things like 'bad compass health' warnings). The only real issue with non-3DR versions is the after sales support you get. I believe the hobbyking HKPilot32 is recommended - mainly due to the great after sales support they provide. Not so certain about other suppliers - mine was from banggood.com - when I reported an issue - they did get back after a day asking for a video showing the issue, but then I upgraded the F/W and the issue went away. Still occasionally get the bad compass health warnings though (I am on Arducopter 3.2.1 f/w)
mackar - I have to ask - did you go down the BLHeli route? I initially did with Turnigy Plush nfet 30a escs (SiLabs based), and had terrible issues where the ESCs would not initialise on power up (after pressing safety button, which I eventually disabled this feature and removed the button - just plain annoying!) I read reports of others having similar issues with BLHeli (specifically on SiLabs based ESCs). The latest version of BLHeli introduced a bootloader (with the idea that you will soon be able to program them over the servo cable), and on powering the Pixhawk - it seems sometimes to force the ESCs to boot into bootloader mode instead of normally, hence the issue with the ESCs not initialising. Its only on the Pixhawk this seems to be seen. This results in the situation where when you arm the craft, the motors do not spin - sometimes just one or a few of the motors are affected, sometimes all - really random. I think what I am trying to say, is - if you haven't already gone down the BLHeli route, I would probably suggest you avoid doing so with Pixhawk. I ended up replacing my ESCs with Hobbywing X-Rotor 20a as a result of flashing BLHeli on my original ESCs, so a costly mistake. The new ESCs initialise perfectly every time - seem to spin the motors far smoother also than the BLHeli Plush 30a did. I think BLHeli is great for small racing quads where active braking works really well, but not so sure its a good idea for bigger craft/motors. APM project also suggests you should not enable active braking on ESCs (and only use medium timing) for use with pixhawk, and that's often the reason folk move to BLHeli in the first place. Just thought you may benefit from my experience. My quad is here:
I have ordered the arms from the z600 to extend the motors out - will give more clearance from the canopy I fitted and for 11" carbon props I now have. Only running on 3s though (not 4s as your's is). 4s for me would kill my motors unfortunately - I don't think a 4s LiPo would fit in the centre either, where I have mine. I have the underneath freed up for a 3 axis gimbal. With the cover off it looks like this:
(well it did before I replaced the ESCs and fitted the canopy, oh and before I crashed it and wrecked my retract brackets, which I now need to re-make, once I get the carbon fibre sheet delivered)