Haven't gone through the whole thread yet so I don't know if these issues have popped up but I just wanted to mention that I updated everything to the latest version (I didn't have it functioning previously because I forgot to install the TWLNAND CIA) and am having a few minor problems playing games off the microSD card in my New 3DS XL.
I'm running the latest stable 6.6 release of Luma, the latest A9LH, etc. Games just have rather long load times (I tried New Super Mario Bros. and Super Mario 64 DS - the former is so slow that it appears to freeze on a white screen when booting, but the 3DS itself isn't frozen) which might just be because of the relatively slower speeds of SD cards compared to cartridges, but there is also audio crackling. My R4i Gold, however, runs absolutely fine when booting through TWLoader, as if I had just launched it from the home menu. Clock rate settings in TWLoader make no difference.
Also, TWLoader keeps trying to download missing box art whenever it boots. I assume it's for my flashcard as that's the one of the three that doesn't have any art associated with it. It's too fast to read properly though, but it looks like it says it's getting box art for Mario, so that's odd.