I'm back!
So, err, yeah, those updated packages will really happen sometime soon ^^. With a bit of luck, I'll manage to break things in new and interesting ways (after all, I did manage to run a rm -rf Kindle from the wrong directory only yesterday, so, yeah, NOT RUSTY!

)
Don't expect much activity from me for a while though, I have something like 4 months of posts to go through... -_-".
And to answer the repack question, provided you don't need to change the content of the package, the easiest way is probably simply to do a double convert (.bin => tgz, then .tgz => .bin), no need to even extract it (which helps avoiding directory structure issues, depending on how you repack it, and potentially double/wrong sig/dat files, if you happen to be running an old kindletool version).
Basically:
Code:
kindletool convert update_blah.bin
kindletool create ota2 -d kindle5 update_blah.tar.gz update_blah_repack.bin
IIRC.