This is a fun project, and it's great. I had dreamt up something similar (I've already bought a couple of 6309s on Ebay), I only lacked the time and courage to try it. Discussing the idea with a guy who had taken a pretty deep look at the code, his opinion was that you'd have to do a very thorough rewrite, which would make the project cumbersome.
Another potential problem is that, strictly speaking, with the higher CPU clock some of the peripherals are accessed out of specification (AFAIK the 6850 and maybe even the timers, haven't looked it up again), so it might not work on any and all M1000s. But it's definitely worth trying, and I'll do that as soon as I get round to it. Once again, kudos for starting this brilliant hack.
Mind giving us a bit of geek porn, i.e. more descriptions on what you actually did and how it works code-wise?