Hi,
yes, if you use 8580/6582s and drill some ventilation slots or holes, it *should* be thermally ok, there was a forum poll a while ago, where some people said, it is getting quite warm in there, so i´d generally not remove the fan hole, just in case you want to add a fan later on. You can put a fan grill on it, to "close" it, even without fan.
Regarding knobs - I´d recommend you wait for a new bulk order by Martin/Kristal to get some of the awesome Waldorf knobs - they fit really well on the MB6582 and are highly recommended - otherwise, any other "industry standard knobs" with 6mm D-shaft will fit.
The expansion port is a standard 25-pin sub-d breakout port, to attach any internal headers you like to external gear. Adding that port is also recommended, as you might like to add analog filters or external voltage controlled amplifiers later on!
Edit: if you are thinking about a very useful mod to the back-panel, think of adding an improved-diameter hole for a professional 6.3mm mix-out socket. That mod is described in the photo tut on page three or so.
Many greets!
Peter