Discovered something useful: turns out I had the launcher for GW was installed, and yes, that was why the profile trick didn't work. Also installing the launcher.dat from the SafeB9S installer was a bad idea as well, as making sure no launcher.dat file was in the root of the card is what enabled it to run correctly. Basically I did the regular 4.xx option on my DSTwo flashcart, did the profile trick, and everything worked...now until i get to the next set of problems. Still following the guide just giving an update that things are moving, albeit slowly.
EDIT: I updated the system firmware to 11.5...I have no idea if I'm screwed or not. It is still working just fine, but should I have downloaded a lesser update from the internet before making my update? Also, anticipating the worse, I made a backup of the sysNAND using GodMode9, and just to be safe, I made another backup of the firmware after updating the 3DS, and installing the CIA files, and running (and deleting) the ctrnand luma 3d update like it said in the instructions. On an unrelated note did see a browser AFTER the update...no idea why I didn't see it before. Might not have had it after-all. :/
Also, and this is really important, how am i to get my backups to run? Do I use GW as normal, or what? The guide just ended without really answering any of my questions, so knowing what to do next is kind of crucial. I inserted the red card, did the profile trick...and it didn't work. I'm not sure what do do with this one. I still got the blue card thankfully, so I could just reinstall stuff. I could do that, but since GW is not compatible with 11.5, that sounds like a bad idea to me, so I'm putting things down for now until I can figure out how I can get my backup working again.