Gonk I may be wrong but from what I understand a A/V processor needs to be able to handle HDMI 1.4 in order to pass 3D I didn't think the 990 could do that (didn't buy the C8000 for 3D but since it's included I might as well play with it).
HDMI v1.4 is not required to pass 3D. You need to have enough bandwidth and a signal path that doesn't misinterpret the video signal and mangle it somehow. HDMI and DVI switching options have been around for a while that offer the bandwidth required. If your unit uses HDMI and is manipulating the video at all, it needs to know what to do when it encounters 3D (which would probably be "leave it alone and repeat the signal to the output). Neither of those force you to be using HDMI v1.4 transceivers, although the presence of v1.4 should be the best indicator we will have for a product that should support 3D. (It's still not a guarantee, as in theory you could use v1.4 chips and have a video section that can't handle a 3D signal.) The problem with feeding 3D through non-v1.4 gear is telling which products can handle a 3D signal. Because the 990's DVI switching is simply a switch, it doesn't care what the video signal is. As long as there's bandwidth to pass the full 3D signal (which I think it very possible), it should be able to do it. As I say, though, I don't think anybody's tried it yet.
Didn't really figure any main stream manufacturer's BR would have a good analog section but maybe technology allows for this so will give it a try. Is there a 5.1 wiring harness available for this?
The best way to do 5.1 analog is just to get six analog audio cables or three pairs of analog audio cables. Folks like Blue Jeans Cables and MonoPrice offer them in packages.
I had to go check if I had any speakers set to small since all mine are rather large but apparently when I set this up a couple of years ago I chose all small plus subwoofer. I'll read your setup guide for the 83/990.
Even for very physically large speakers, small is usually the best setting to choose (along with a good choice of crossover point).
I emailed Oppo a couple of weeks ago asking if any of their BR's could be updated to 3D and he said they were looking into that but it didn't look promising, I only asked because Sony BR's and PS3 can be upgraded to 3D via firmware. Since I got the 6900 for free I might still get the Oppo 83 sometime unless it's getting a little dated, or Oppo comes out with something comparable.
The PS3 is basically a little HTPC with plenty of processing horsepower, so they have been able to develop 3D support for it. The standalone players that are getting firmware updates to enable 3D were designed from the ground up for 3D and were simply released before the 3D firmware was ready. The BDP-83's hardware was finalized in late 2008, long before anybody was even thinking about adding 3D to the BD spec. My expectation is that we won't see 3D support on an OPPO player until they release a player designed around the new 3D spec. It's very possible that just such a player is in development, but we've not heard anything about it yet.