You'll find out one way or the other soon enough, but dropping a cylinder is very obvious on mine. Having a 50% misfire I think would be quite unpleasant. But once you have your system working, it's entirely under your control whether you run the 'steam cycle' every other cycle or every third cycle or whatever.
Since you're injection into the chamber at TDC you'll have a lot of pressure working against you. Have you worked out how you're generate enough water pressure? I suppose a diesel injection system would do it, but they're notorious for suffering catastrophic failure as soon as you run anything but diesel through them so I'm not optimistic that would last long. I've never played with diesel injectors but petrol injectors have a relatively short life when used to inject water due to internal corrosion, and I think limescale deposits would cause problems pretty quickly unless you use distilled or deionised water. That would bump the cost up dramatically. I use small quantities of Methanol as a corrosion inhibitor / antifreeze and that would bump the running costs up too.
So, from what I can see so far the mechanical parts of the water injection system present the main challenges.
I don't think there's any reason to be concerned about over-cooling the chamber and interfering with the normal ignition / burn sequence. I've seen some studies of the effects of combustion chamber temperature against power, and power output was more or less completely independent of block/head temperature. When it's running the inside of the combustion chamber will normally be over 100C and so there's no chance of having a cold damp combustion chamber, and I don't think that dropping the metal temperature a few degrees is going to make any difference.
It sounds as if you have got the petrol injection cut-off sorted out but I'm still not clear how you're going to time the water injection. I get that you can trigger it from the spark, but you need to know which of the pair of cylinders is in the compression stroke. I suppose you could monitor one of the fuel injection pulses and work the engine phase out from that, if you know where the fuel injection pulse occurs in the engine cycle.
I assume you would enable this whole water injection system when the load and revs corresponded to cruise conditions and leave the engine to run normally the rest of the time.
Do you have any sort of cat system or EGO feedback system on this car? One thing EGO sensors don't like is having fluid dumped on them, and the missed firing cycle would throw any EGO sensing out of wack. Suppressing the fault codes is one thing, but if your ECU relies on an accurate EGO signal then it won't be happy.
Given your experience working on engines, I'm sure you must be tempted to try the full 6-stroke conversion. 