Water vapor in the gas line isn't really a problem at all. If I could get enough vapor, I wouldn't need water injection! It does help with output, and if it is 1/4lpm, that can add up pretty quick if it is per cell.
The more I think about it, the more I like the idea of plumbing it into the intake with the vacuum based check valve. The only real issue I see is slow deceleration to an idle. If that becomes a problem, I may rig up a way to shut off 3 of the 4 cells off at idle...or more specifically, vent their output to the atmosphere. If I mechanically close off the flow from 3 cells but don't shut down the current, the cells will keep producing. I have an idea of how to store this production at idle and dump it into the intake during acceleration. Accelerating from a dead stop is real hard on mpg.
You won't need to rewrite the eproms. That is really overcomplicating things. I don't know about your toyota, but on my ford I plug a usb cable into my laptop and I can literally adjust any parameter in the computer. It may not be quite that easy with the toyota, but I bet there is a solution other than rewriting machine code (which I can almost guarantee it is). I was originally in programming too until I switched careers....couldn't stand the cubical life.
The simplest thing I can thing of is design it like a diesel based natural gas engine...throttle your air intake with the throttle body and throttle the fuel with a smaller "throttle body". This is a simplistic form of the natural gas engine, but i bet it would be good enough for us. Not including an IAC, the throttle body doesn't completely seal and has a small, measured air leakage. To get your fueling at idle set right, you could slowly enlarge the hole in the butterfly and then just sync up the openings of both throttle bodies. Adjusting your fuel mixture would be about as simple as loosening or tightening up the cable to the fuel TB. Where to mount an additional throttle body is a question, although I have an idea. Take a look at this TB.
http://tunertools.com/prodimages/BBK/3502_large.jpgThat is basically the throttle body off of an old 302 ford truck. They are dual inlet like that stock. The throttle body is pretty good size and mounting that up to any other engine would just take an adapter plate. Hook one up to your air intake and the other to your HHO production. They both work off of the same cable. The butterfly for the HHO could be drilled out and different sized orifices screwed in to set idle speed (similar to carb jets, we use them at work). Fuel mixture could be adjusted by rotating the butterfly for the HHO on the shaft.
Your dream of running on pure HHO that you generate isn't based on production, but the assumption that you can get approx 80% more power from burning HHO as creating it...and that is a very strong assumption. If you are able to run pure, I would still just block off all incoming air and let the throttle body do the work. Idle speed could be adjusted the same way I said above for fuel mixture. Running HHO, however, isn't just the fuel..it is the fuel and oxygen combined. It is already in perfect stoich and doesn't need to be precisely regulated like gasoline injection does. The throttle body just regulates this stoich entrance into the engine, and thus the power/speed of the engine. Putting your injectors on a switch and running HHO right into the throttle body would be all you need to do....run out of HHO, turn the injectors back on and take the tube off the generators and hook the air box back up, something that could be done on the side of the road in a couple of minutes. I really don't see any benefit to pumping it into the leaky airbox if running pure. Running a pipe from the boubler to throttle body, it could be sealed up to several PSI. No worry of leakage.
As far coming to a stop and low idling, one idea could be to rig the generators to pump into a large propane tank, say 20 gallons or more, and the throttle body draws off of that. When stopped, the generators keep pumping HHO into the tank and upon acceleration, there as an abundance of HHO there to help accelerate. Acceleration will take the most fuel and really tax production, having a bit on reserve can't hurt. You could pump this tank up to a decent pressure before venting, say 50psi, but there are a lot of variables there.
As far as running on pure HHO or even a very high percentage, no one has a lot of experience with that to really take educated guesses right now. The engines that have been ran on pure HHO haven't be ran long and there isn't too many people running around running on a whole lot of LPM. I think that if it is possible, it will be fairly easy. The majority of problems comes with getting the right fuel mixture all of the time in every possible circumstance. We already have the proper fuel mixture, the only thing we have to worry about is delivery into the engine...which is a pretty small problem once we have the LPM to actually do so. In all of my tuning, I haven't ever spend much time on setting timing, a solid 90% is tuning the fuel mixture. That part is done for us.
By the end of summer I hope to have an educated answer. I am pretty pumped up about this (spring fever already). I am building 4 more cells as soon as my parts get here. I have a small briggs that I will play with. Step one will be getting it to run off of the HHO produced by a few battery packs and charger. Once I see that it can run and with what LPM, I will start mounting alternators to it. A single 200 amp alternator will max this engine out in power (I believe it is a 3hp). Will, say, 15lpm power this engine under full load? Seems like it should, and I have seen a lot thrown around the net on it, but it is hard to know what to believe. Whatever works with the briggs will work on a larger scale automotive. If it works for the briggs, it should work for anything. If it doesn't, it won't. That is my theory. It is hard-impossible to mechanically change timing on the small engines, but I have a few tricks to try. Worst case scenario is installing a trigger wheel and one of my MSD boxes, but I think I can get away without doing that...