My gut is also that you'd be okay as long as you keep the loads evenly distributed, run in I-3, don't try V-2 with cylinder 1 and 2, do 3-4 or 1-6, 2-5 instead (though that would probably be real rough) V4 could be 1-2, 5-6 or 1, 3-4, 6 or 2, 3-4, 5. You probably wanna just stick with a simple I-3 though.

Roadwarrior...what are your plans for the voyager...you mentioned earlier that you were planning a DOD system.
What arrangement would you have and how would you set up the switches?

I'm just going for I3 on either bank, so I'd have a switches for cutting out either side. I am just going to play around with it as I go really... one advantage I have is that the O2 sensor is right at the Y junction of front and rear exhaust manifolds, this means that the higher pressure and temperature exhaust flow from the active bank will tend to expand around the O2 sensor, and shove aside the "fresh air" coming from the inactive bank. If it was any further down the tube the flows would mix better.

Hopefully I'd work towards a mostly automatic system that triggers on load, temperature, vacuum etc... so then I'd have switches for V6, I3 either bank and auto. Whether I'd set the auto up to alternate banks or not, depends on what I see when I play around, whether one side "wraps round" the O2 sensor better, whether one side will go cold too quick...

I'm also thinking that ideally I want to put on a dual throttle body setup, with ability to close the TB on the inactive side, this motor seems to give little drag when engine braking with the throttle closed at lower revs, I'd equate it with turning the air con compressor turning on, maybe ~2HP for the whole six, so that would be about 1HP drag with one bank in vacuum. Whereas sometimes shifting down with light throttle applied (i.e. not giving it enough pedal to rev match) seems to give twice as much engine braking as closing the throttle all the way.

Since I'll be messing with the wiring anyway, I'm also pondering putting in forward biased diodes that can be switched in, in series with the injectors... the point of this would be that silicon diodes drop 0.6V, and lower voltage to the injectors increases the "dead time" slightly, meaning that the actual open time will be reduced, i.e. changes the pulse width without the ECU knowing about it. This might be useful to lean back the injectors if the ECU sees too much O2 and puts in too much fuel. However, some O2 sensor trickery would probably be preferable, hence why I was thinking I might need to stick an O2 sensor in each manifold and switch between them according to shich bank was running, and average, or switch back to original in 6 cylinder mode.

Here's a quote from P.70 Popular Science, January 1977 about Ford's early DOD efforts on an inline 6, that gives us some clues...

I'm planning to use that as a guideline for the automatic version and read the TPS for throttle angle, (or rig a cam and a microswitch) read the TC lockup status instead of checking it's in high gear and up to temperature and up to speed, and read the MAP sensor, or add another for checking vacuum.

Like your plan.
I'm thinking of just keeping mine purely manual...literally displacement on demand (DOD)...though I may make up my own acronym hehe.
Maybe Variable Cylinder Control (VCC) or Variable Displacement System (VDS).
Also, at this stage I'm not planning on sealing off the inactive cylinders...hopefully will still see a FE inprovement. if not I'll look into it.
Also in response to theclencher, it is not just of matter of unplugging the injectors and going for a drive because, and I've tried this, it makes the car veeery slow off the mark, horable to drive untill up to speed and is propably not good for the engine under such loads. If these ideas are going to work the injectors needs they need to be switched off at cruising speed where they will have the greatest effect on economy. The system will also need to deal with the Oxygen Sensors somehow because to not would propably negate any gains due to the ECU compensating by adding more fuel.
I think the debate now is weather any of this will relise any usefull FE gains and this is something that can only really be established through testing and trial and error.

Yeah, really needs to warm up on 6 cylinders before you switch to 3. Although if gas doubles I might just unplug 3 and remove the lifters and knit a woolly sweater for that side of the block.

Gas? Double? Never!!!! LOL.

IIRC on the production DoD systems that GM and Chrysler are using, they have to close valves on the disabled cylinders to prevent the engine from pumping the extra air into the catalytic converter, which combined with the unburned fuel from the operating cylinders would cause a very lean condition in the cat and cause it too overheat. Or am I way off base here?

That's possibly more necessary for new vehicles due to cats getting more delicate and having less palladium and platinum in, spread over more area...

If it's a problem could always remove the CAT...I need a new exhaust soon anyway

Ya know, before you guy's get to carried away with your gut feelings and cylinder deactivation, you might want to research some older threads which have pretty thouroghly hashed all of this out, previously.

In short, unless you can find some way to disable the valves, just shutting off the fuel flow is not going to make any improvement. If anything it is just going to cost you more, to have it run worse. If you are going to do anything, you need to have something like a VTEC, where you can switch to a second cam profile, which doesn't open the intake or exhaust valves. Anything you are trying to do, otherwise, is most likely going to waste your time and money. MO, FWIW