Hi mate.
Yeah, The completed Pass / Fail list should save you some pain.
I will probably donate my entire karma to you if you test out and fix Tiny X on the 3 first

Also note that the GIT repo from BR will change over time - so perhaps take two copies (one for reference, one to update via git pull, make diffing easier later on)
I run
4 5 copies atm for similar reasons (multiple targets, copies etc)
not terrible advice.
remember to configure your device as outlined at the minimodding article and if you are going to get radical with Busybox or something ensure you go down the safe path and don't end up with a bazzilion files (I did that once) - or copies of the busybox binary over and over. check my better busybox thread for the link / alias solution if you feel the need to replace core functionality. its much safer and takes up less room.
much of the stuff in /lib (not /usr/lib) /bin and the other ROOT folders will NEVER be called as it is core the the device (and has copies on already) so figure out what you DON'T need to copy (copying takes time, transfer the FAT can be dull the 1000th time, keep it trim, don't copy redundant rubbish)
/usr is probably a really great folder to start with and go from there.
readelf -d (theApp) to check any missing bits (try just dumping it on and see what fails)
a LOT of the time, it will "just work" with the minimodding config. (and just the /usr content moved)
another trick is to prefix the stuff with /mnt/us is the makes (I now do this on the new added stuff) - but let's visit that later - when you have a file skeleton to reflect that location.
more tips:
Don't build the QT examples. (circa 2 Gb IIRC) or at least do it last. and separate out the files (usr/share/qtX/blah, I think) before passing via scp.
moving files:
WinSCP has a nice trick of unrolling all symlink on-the-fly by default when copying onto FAT via Wine. I recommend it.
finding output:
I also no longer even build an output filesystem (tarred or otherwise), I simply jump to <~/GIT/BRK3>/output/target - those are the files you want for the kindle.
splatter them (ignore everything except the /usr/* in most cases) onto FAT mirrored as-is (so often you just copy that one folder for an updated transfer of a build) and since WinScp manages all the symlink resolves... well.. cup of tea and its done
Best practices:
Originally took me maybe 20 mins of "titting about" using other methods of transfer and by-hand sym-link resolving. Honestly - the method I'm describing is MUCH quicker.
for getting "to test". (if you feel fancy later on you could rsync it or something

)
It could be scripted - to 99% success - if you preferred that route.
I'm happy with cherry-picking files and fast unrolled links.
HTH.