The 5-stroke Engine

Go for it. Hire a shark shyster lawyer.

You can patent a rock. Bo$e does it all the time. The waveguide radio is nothing more than a 1/4 wave transmission line,developed in the 1930s, and poorly designed. Given enough lawyers you can do anything.

Yes, you can patent anything, even the same basic "thing" as patented before, you just have to change the appropriate wording and a few minor descriptive details to prove that it is "different" that existing. Just be prepared, if applying for a patent, to spend lots of $ on lawyers, if your idea is even close to something else already having a patent. The fewer the patents "similar" to yours, the easier(<$) it is.

The animation on the Ilmor video seems to show a strange firing angle - it looks as if ignition is shortly after BDC of the HP cylinders. Is that correct, or artistic license?

No, not correct. I don't see any spark plug here either, so it's rather diagrammatical. They've colored the exhaust "red" at the wrong time in my opinion. The 2 high pressure cylinders are just normal 4-strokes, 1 & 3 being 360 ^o out of phase with each other, so that they exhaust alternately into the larger low pressure cylinder (2). Cylinder 2 is therefore a 2-stroke, having a power stroke every 360.^o

Obvious configurations would be a V-6 or flat-6, but I proposed another configuration that I thought was beneficial - a 6 cylinder but with the length of a 4-cylinder, and only slightly wider, so that it could fit existing 4-cylinder engine bays.

That's what I thought. Looks a bit like they're conflating the petrol cycle with a diesel cycle (i.e. just showing the air/fuel mix getting hotter due to the compression). Odd.

I have often wondered if this design could be improved upon. For instance, tuned exhaust or modern ignition. I was told this design had advantages with lower octane fuels. (Ethanol?).

The pistons appear to be mislabeled.

Yes I was aware of the Puch Split-single engines and those by DKW. You are right about the mislabeling of the pistons, although it really doesn't matter which way round the engine is mounted, so I don't even see the purpose of labeling them forward/backward. The idea goes back to 1912 and some of them (DKW) were quite successful. But they are 2-strokes and have the attendant exhaust pollution problems:

http://en.wikipedia.org/wiki/Split-single

There is another so-called "Split Cycle" engine - the Scuderi. If you look at this and listen to their over-long description, you realize that its just a supercharged single cylinder, the supercharger being the adjacent cylinder.

https://www.youtube.com/watch?v=BK2Mm7TYHuk

As ever, nearly everything has been tried, yet we still have the same basic design I.C. engines regardless. But you are right in that some of these might benefit from modern ideas and technology - even the (stolen) Gerhard Schmitz 5-stroke design.

This is what I had in mind when I mentioned tuned exhaust:

It may that these acoustic principles would apply to the cross-over for split cycle.

Re. Scuderi Engine: My description is not accurate - it is not the equivalent of a supercharged single cylinder - there is no supercharging. It is, as described, a "split cycle" - 2 cylinders doing the function of 1. Silly me.