Hey all. That side job I mentioned is finished, so I can probably crank out an update sometime this week/end. I can't promise that I'll have time to finish Bukkit compatibility, but (given how much trouble some of you are having) I'll definitely implement an easier way to find your Autominers and better ID collision handling. There might also be a new fusion fuel for you to play with. This is unfortunately going to be the last update for a while - my qualifying exams (aka, the second-most-terrifying grad school experience, right below thesis defense) are on the 25th-27th and I'll be spending the intervening time with my nose in various books trying to prepare.
(Also, regarding pipes - I'm not familiar with Buildcraft or similar mods, but if there's an API I can use, I'll consider adding pipe compatibility in the next release)