@Huck:

Sorry, all I've ever worked on was gasoline-powered, some air-cooled, most not. I can't think of a single time a customer came in saying "Can you make my Mercedes TD rally-capable?" (But I think I would have had a
*lot* of fun with that...)
They (MegaSquirt)
do have an exhaustive set of forums (would that be fora? Latin can be so confusing, sometimes...) for support, not just from the builders but the guys (like me) who've used the things. they encourage experimenting - and how! - but I'm willing to bet that if you mention HHO power you'll get so much static - interference and argument - and very little assistance. So it's probably best just to see if the thing does diesel --- and I can't think of a single reason it wouldn't. Heck, the parameters are fully scalable, so I figure it would probably work fine, even make you proud.
@jpshydro: Any time, just pointing out options, is all. I know how much trouble my Subaru Outback was when we flashed the ROM in it, ended up "upgrading" it to a WRX ROM, performing some amazing electronic fakery so it wouldn't go into "limp-in" mode because the turbo appeared to be missing. No, I haven't turbocharged the Outback - yet - I've been busy seeing ho far I could push it with natural aspiration. More on that, later... Fuel has become expensive, so the thought of cleaning up my emissions, adding a little pep,
and improving my MPG has me performing "other" experiments, of late.