I don't really think the problem is in the SD card... Sincw you can't even get to load the hbl, I'd try clearing the cookies and data for the browser, then try accessing it again. Or maybe instead of self-hosting, try accessing the wiiubru site?
I'm guessing it's more stable? Also, if you get a firm folder don't place it to rxTools/sys but directly in your rxTools folder :) And there is no need to create any rxTools launcher.dat file, it's only used to start the gateway menu.
You can create emunand by downloading gateway's launcher.dat, then use either the nintendo ds profile exploit (mset) or browser exploit to install rxTools :) you xan keep your sysnand firmware as it is and continue using the mset exploit to access your emunand after that or use sysupdater to...
did not know that could even happen by using cartridges to update :/ I updated my console with LoZ: MM and had no major problems installing rxTools, so I guess I got lucky there :D
Just make sure to clear the browser history and cookies before you load the link. Also, if you'll use the rxTools build @Nestar recommended, use http://launcher.rxtools.net :)
The rxtools.net works for pre 3.0 builds that still use rxTools.dat, the github if you have a 3.0 build. I had the same problem, but either the MSET method or what @Nestar said should work for you. The problem is that updating via gamecart doesn't update your browser, so it doesn't work...
It would be better if you'd install your games to emuNAND, since you can update it to the latest firmware and then update games via the eshop to play online and stuff.
Now set up themehax as it is described in the tutorial. Just instead of step 7 where it says to do
Change timeout to -1. That way, when you start the 2DS you'll get a menu and you'll be able to choose whether you want to start homebrew or rxTools :)
Well you have nothing to be afraid about if you selected devmenu :) Just make sure that you keep your 2DS plugged in during the update, so it doesn't turn off.
You should install sysupdater to sysNAND, not emuNAND, since you'll be updating your syNAND, not your emuNAND :) So install the sysupdater cia to your sysNAND :)