Scott, we'd have to measure and then model the flow numbers to confirm before hacking up the front bar again, but it may be a worthy consideration depending on the IC's basic design.
Generally it makes SFA difference, but at high boost where the compressor is forced to a higher pressure ratio for a given system flow rate, there can be significant change in actual density at the intake manifold - enough to warrant reconsidering your intercooler setup.
The cams aren't really a concern, we can get them modified without any real headaches. At this stage i wouldn't be concerned with the engines base flow profile, i don't believe its an issue unless you go up a full turbo size (ie. GTX35).
I think what saves the VQ series engines (and VG series) is the broad, well angled ports - fantastic potential for big flow numbers. Plenty of port volume and average ID. So, the heads do OK even with baby cams, which from an emissions point of view is exactly the reason Nissan would have stuck with the design.
There's another IC you should consider, i'll have a chat to you about it next time i pop by.
RE the SLD, its a quick install on the Toyota ECU, direct to the loom. Can't be that bad, we'll figure it out.