If you are using Emunand I seen cases of System being VERY slow in general with original 3DS XL. Had a case where I used apparently very slow 16 gig card on a 3DS with emunand. Since A9LH and guides to install it end up not using emunand, then it is the card.
This is weird if it was fine before but now is not. Reformatting the card might help though. Since you had to have emunand on the card during your process it might be funkying it up. Otherwise it is most likely the card and you just now having more there than you used to. In my experience normal format (Not specifically 64k cluster) class 10 64gig XDHC has been very fine. SOMETIMES the system will just take extra time indexing the home menu, this is random (sometimes few of my titles are not there for few moments, these are somewhat normal all things considered)
This is weird if it was fine before but now is not. Reformatting the card might help though. Since you had to have emunand on the card during your process it might be funkying it up. Otherwise it is most likely the card and you just now having more there than you used to. In my experience normal format (Not specifically 64k cluster) class 10 64gig XDHC has been very fine. SOMETIMES the system will just take extra time indexing the home menu, this is random (sometimes few of my titles are not there for few moments, these are somewhat normal all things considered)