Interesting results! 
I looked at the atpower website www.atpowerthrottles.com and saw a lot of their kits put the throttles as close to the head as possible. Wonder if that works a lot better than putting the throttle on the end of a manifold?
Maybe worth looking into on CFD to see if this is a viable alternative. It would be much cheaper to just make an inlet flange and adapt individual throttles to it and make the inlet trumpets have the shape to clear the hood.
Just throwing another option out there. I love the ATPower stuff, but its $$$$!
Whenever someone equips ITBs they always talk about how the throttle feel is "better". The reason people have this perception is because of a transient effect between opening the throttle and the air reaching the engine. The lower you are in the RPM the more obvious this effect is, which means that even if ITBs are poorly set up they can still improve the 'connectivity' a driver can experience. The major reason for this effect is the distance ITBs are placed from the ports - rather than actually being ITBs.
I'm going to use some exaggerated numbers to explain the effect just because it is easier to visualise.
Imagine a situation where you have a throttle 100m from a port, and another where you have the throttle 1m from the port. In both situations the throttle is closed, and then instantaneously opened. In both cases there is negative pressure on the engine side of the throttle which pulls air in at 100m/s. You can see that it would take a full second for the longer runner to reach the engine before providing power, whereas the the 1m port would take 10ms (actually in both cases it would take longer, but the actual effects aren't really worth discussing, I'm just making a point). 
Now keeping in mind that there is a massive time difference before the power comes on; let us assume that the 100m throttle is actually better set up and creates more power and torque. You can see that even if an ITB is poorly set up in terms of power, it can have a very real effect on drive-ability. This is why even in poorly set up systems people will still talk about how much better the throttle feels. This 'feel' literally comes from the distance you place the throttle from the valve opening. It also has more of an effect at lower RPM because the intake velocity is lower and takes longer to traverse the distance. Closer may be better for feel, but there is more than one effect at play.
There are other considerations, such as injector placement, throttle by-pass and vacuum lines that need to be accommodated on the manifold. And then there is the fact that this is intended to be useful on road cars as well. In terms of flow, the longer the distance you have to transition from a circular butterfly to the port shape the more laminar the flow will be which will improve cylinder filling characteristics. The analysis I've shown only shows the butterfly at WOT, but if it is partially open there can be significant turbulence which reduce fuel vaporisation, so if you place very close to the oval port you will induce even more turbulence in the profile transition.  The manifold we're designing is to be part of a tuned-length intake as well, so the whole system should resonate with the RPM to assist in sucking in more air.
The 'ideal' ITB set up is very extensive. You would have dual stage injectors, with one on the port side of the butterfly, and one on the intake side. You can generate significantly more power by injecting fuel further from the port, but this only works at WOT and high RPM otherwise the fuel won't get carried all the way into the engine and you can get a flame-out into the engine bay. You would place your ITBs with about 100~150mm distance from the valve to allow a smooth laminar transition into the valve profile. 
This smooth transition is very very important, and it should highlight why I'm not keen on products like the dbilas ITBs. In the simulations I just posted up, a change in curvature that changed dimensions only a few mm results in a 1% reduction in efficiency. If you look at dbilas their kit has a sharp kink with no curved transition, which would have a very significant effect (I'd be willing to wager 10% or more) on reducing mass flow. You encounter the same issues when using an adapter plate. You would need to make an adapter plate 25~50mm thick to get an appropriate transition to maintain laminar flow - which would end up having defeated the purpose of putting the ITBs close to the port in the first place. It would be different if the butterfly was the same shape as the port, but it is circular and you need to accommodate that change in profile.