Questions on new loop

I'm going to be assembling my new loop (hopefully) next week and have some questions. Here's what I'm thinking of:



Bigger: http://i.imgur.com/fdgG1ED.jpg

Components:
Phanteks Enthoo Primo (Black/Red edition)
Delidded/Lapped i7 4790K with XSPC Raystorm (Black aluminium bracket + Red faceplate)
ASUS Maximus Hero VI (Black/Red, Thanks to Dangman for the suggestion and mothman for the input)
G.Skill Trident X 2400 (Black/Red)
MSI 290X Lightning with EK Full Cover Block + Backplate
Antec HCP-1300 Platinum
Samsung 850 Pro 256 GB
Crucial M500 240 GB
16x Corsair SP 120 Quiet Edition (With red rings)
Reeven Six Eyes II Fan Controller (Thanks to Tsumi for the suggestion)
2x Hardware Labs Black Ice Nemesis GTX 480 (Thanks to Tsumi for the kickass recommendation)
XSPC D5 Photon Pump/Res
Primoflex Advanced LRT (7/16" ID, 5/8" OD, Bloodshed Red)
(No optical drives, just the fan controller. No spinning disks either.)

My questions are:
1. Will the D5 Photon fit there? The Black Ice Nemesis GTX 480 is 54mm high so with 25mm fans in P/P it would be 104mm total. Also, the MSI Lightning 290X has a slightly higher PCB ( http://i.imgur.com/7yi5lv7.png ), so would that prevent me from fitting the side panel on or even installing it?
2. Would there be any other good place for the res/pump? I can't mount it where the res bracket is ( http://cdn.overclock.net/e/ee/500x1000px-LL-ee575342_P1010034.jpeg ) as the lightning is almost 12" long. I am going to either run with the side piece that holds the optical bays off, or mod it like this btw (due to rad being extra wide): http://i.imgur.com/P42vQsQ.jpg
3. Depending on questions #1 and #2, what's the best route to take so I don't have tubing going all over the place and looking like ass?
4. One thing I'm a bit held up on is the rads since they have a front-back flow pattern instead of left-right: http://martinsliquidlab.i4memory.com/img/HWlabs480GTX2PassFlow.png Should I be concerned with optimizing this or does it not matter as much since I have the fans in push/pull config?

Any input would be great, thanks!

Loop order does not matter. What matters is having a sufficiently high flow rate. Route your tubing to use the least amount of tubing possible.

I would optimize the flow of the GTX radiators, though I'm not certain the Nemesis GTX radiators have the same flow path as the older GTX radiators. The cooler side (outlet) should be closest to the intake, the hotter side (inlet) should be closest to the exhaust for optimized heat transfer. Though in all practicality I'm not sure it matters much.

Thanks. I got a lot of my answers from another forum but I was going to configure the rads so I would have push = hot side, pull = cold side but since you've explained it, it wouldn't make much sense to use hot air for the cold side compared to cold air for the hot side.

Are the inlets and outlets interchangeable like on other rads? Martin said you can stick a pen down each hole and the one that sits higher should be used as the inlet. Why is that so?

Assuming the rads have a dedicated inlet/outlet and aren't interchangeable, that would mean that having two of these radiators, one on the top of the chassis and one at the bottom, each would face the other. So both would have to be intake or exhaust in order to optimize it, right? Should I not worry about it then and just do top exhaust/bottom intake? That would mean that one rad would be optimized and the other wouldn't.

Assuming the radiator is the exhaust of the case:

The higher inlet would be the one on the intake side. This is reversed in the situation that the radiator is on the case intake.

The only radiators that are not interchangeable (technically, they are all interchangeable, some just perform better in one configuration than another) are the Black Ice GTX and Aquacomputer radiators. The U-style radiators perform identically regardless of which port is the inlet and which is the outlet.

So to get the highest performance out of the exhaust radiator, the inlet with the pen sitting higher would be your flow intake. To get the highest performance out of the intake radiator, the inlet with the pen sitting lower would be your flow intake.

If you think about it logically, the higher pen means that that port leads to the front of the radiator, while the lower pen is connected to the rear of the radiator. Radiators do not have any kind of directional flow device.

I think I'm more confused than before.

If I have bottom rad as intake and top as exhaust, then to optimize the fans, one of those rads would have suboptimal flow like you were saying, correct? Because the radiators face each other so the bottom rad has fans blowing from opposite side of inlet/outlet into the chassis while the top would have fans blowing from the side of the inlet/outlet out of the chassis. It seems that having bot as intake tip as exhaust means the flow of one radiator isn't optimal. So to optimize the flow, one of the radiators would have a suboptimal fan configuration?

No, you can optimize it by having opposite inlets on each radiator. I also kind of messed up above.

You want your inlet to be on the exhaust side of the radiator. For the top (exhaust) radiator, that means your inlet should be on the deep pen side. For the bottom (intake) radiator, that means your inlet should be on the shallow pen side. That's the optimized flow pattern for your radiators. If they utilize the same flow scheme as the previous GTX radiators.

Wait, how is that the optimized flow pattern when the inlets and outlets aren't the same for each radiator? That would be the optimized fan configuration you explained, right?

There is no "optimized" flow in terms of which port to use as inlet and outlet provides the best flow rates. There is "optimized" flow in terms of which port provides the best cooling performance, and it is different depending on how the radiator is oriented in relation to the airflow direction.

You're stuck on there being only one flow path. The flow can be in different directions, and optimized cooling flow is different for each radiator configuration.

Okay, I was thinking of it like some blocks where you can technically interchange the inlet/outlet but the flow would be severely impeded if you used the outlet as an inlet (i.e. optimized flow meaning less restriction). Not sure why I thought that but it makes sense now.