re: library, I'm not arduino savvy enough, but help yourself to this implementation. If you can add a function hook to the timer0_millis++ section that the library sets when it is loaded and then coordinate with the timer_0_clock_cycles parts and the appropriate registers then it is doable without using another timer.
FYI, just noticed 0012 was available and I tried loading it. It looks like you can only get the mpguino code to fit with 0011 for now. I really feel like I'm abusing the ide to be running so close to the size limit in 0011 anyway, was worried it might not fit in 0012.
Binary sketch size: 16772 bytes (of a 14336 byte maximum). Is there any obvious things that have grown since 0011 that might be removable? I struggle with the C.