I guess you can get PuTTY for your ssh and sftp needs and then use a third party app to make it transparent. I don't see a reason to use a dos emulator on xp.
It's always nice to do emerge -p --depclean before doing the actual --depclean. In most cases it will mess up your system in one way or another and it's said so in the man pages, IIRC.
You'll definitely need to recompile your kernel (since your new mobo may have new chipset controllers and such). I wouldn't try and reinstall everything unless something goes horribly horribly wrong.
If karamba is masked (I'm not on Gentoo right now so I can't check) you have to add ACCEPT_KEYWORDS="~x86" (I'm guessing that's what was trying to say ;)) before emerging. It's a bad idea to put it in make.conf because it will tell portage that merging masked (= possibly unstable) is okay.
I think it would be nice to have a config app that does the basics. Of course, you can say that flux is not a DE. However, I don't know anyone who doesn't want to have nice wallpaper. Why include a nice way of setting it via the flux menu.
I don't have a problem with setting it manually, I just ...
I think that menu transparency is only available in the developer version 0.9.4
I'm couldn't be bothered to find out how to install it though. If someone can tell us, it would be nice