+1 to using component/SPDIF. Run component video directly from sources to the display itself, completely bypassing the receiver. Now, you should more easily be able to calibrate the display to each source.
The only reason to run HDMI thru the receiver first, outside of convenience's sake, is to access lossless audio. Most sources listed here do not have this, so don't. As for the convenience, it may not even matter anyways, if you compared one click on the TV remote to one click on the receiver remote. If a universal remote, a moot point to begin with.
Speaking of convenience, HDMI switchers will have remotes, and I would prefer that they have discrete codes per input, so you don't have to toggle. That said, it's really hard to beat Monoprice for value.
However, if you go the component video route, which is the one I concur with, you probably don't need the switcher anymore.
Regarding HDMI 1.4, don't worry about it, the only thing it will get you is the bandwidth to send both* 3D video and audio to the receiver. But since all of these 3D players have dual HDMI outputs so as not to immediately supercede 1.3 receivers, simply use that feature. The extra HDMI cable from Monoprice will cost you only a small handful of bucks.
