Hi Stephen,
If you find a bug, you can choose any of the following methods to report it:
1) Make a forum post.
2) If you have a Google account, post an issue in our bugtracker:
http://code.google.com/p/leaflabs/issues/list
3) If you have a Github account, comment on the line of source you believe to be in error, and we'll see it on our Github dashboard.
4) Email bugs@leaflabs.com (which I've just created).
Regarding your question about replacing usb.c, you should be able to make this change in the 0.0.9 IDE release without breaking libmaple 0.0.9. Your use of the word "dependency" is correct here; there haven't been any changes in usb.c's dependencies which would cause geoffreymbrown's patch to break if applied to 0.0.9. However, it is unlikely to solve your problems with SerialUSB.
There are a variety of fixes we've made to the SerialUSB code which should improve its stability significantly. These occurred in the debug-serialusb libmaple branch, which will be merged into the master branch by the end of the week.
At that time, we'll put together "snapshot" releases of the IDE (not a full release, more like a preview) containing the new libmaple code, so IDE users can try it out, instead of just the users of the Unix toolchain. We've recently spent some time automating the production of IDE snapshots, and we plan on releasing one any time we add any important new features or bugfixes, in order to let the community try them out (and hopefully provide feedback).
Expect a forum post when it's done, and we look forward to your feedback!