Can't answer the BibTex question, but I might be able to help a bit with the others. I'm running Xubuntu 10.4.
High load on HDD: is it the drive that's the issue, or CPU/Memory load? On my last computer I had an issue with Calibre creating too many threads for my processor, causing freezing and overheating.
There are settings in
Preferences|Advanced|Miscellaneous called
Maximum number of waiting worker processes (needs restart) and
Limit the max. simultaneous jobs to the available CPU cores. I set the first to "2" and I have the second one ticked. Coupled with recent performance improvements, both of those have made Calibre much more friendly. I still find it responsive, but it doesn't thrash either my CPU or HD.
Install questions: To install (and update) Calibre, I use
the code from its website. I made a simple script and stored it in my
/home/USERNAME/bin folder (I called it
calibre-update.) Now, whenever I want to reinstall or update, I just type
sudo calibre-update into a terminal and answer the single question it asks by hitting the enter key. It installs pretty cleanly into the
/opt directory, but I could tell it to install anywhere else I might like.
99% of files: That's not a system install, using a DEB file, but with the frequency of Calibre updates, you would be severely out-of-date trying to go that route. To work properly with the system, some files have to be created in other directories, eg:
/usr/bin/calibre etc.
I seem to recall that there is an uninstall script floating around somewhere, but ...
found it!
Hope that helps somewhat.
EDIT: there's also a
calibre-uninstall command placed in
/usr/bin -- I just found it, after reading the thread I linked to and trying
locate calibre. I've obviously never used it, but it looks like it does the business. So, between the install script and the uninstall script, you would probably be just fine without a proper DEB.