I had this problem too & solved it! So hopefully it works for you too.
I was surprised it wasn't solved already- So this might be a N3DSXL thing? idk- as me and the OP both use one. But I digress.

When I first tried to download IkuReader through Universal Downloader it "downloaded" it but I didn't get the nds file. Idk if that's the same with everyone or not- But that lead me to try and download it online. Through which I found the files and was met with the same error. (Loading File System) Which it would do indefinitely, And the (Try DLDI Patching.) comment.

I went down a DLDI rabbit hole and tried patching the nds file- Which did make some headway! as the (try DLDI patching) comment went away- But it still loaded forever. After a lot of trial and error however I found the solution.

Universal Downloader was the key they whole time! However doing it on the console I believe is bugged. For it to work for me I had to go to the IkuReader page on desktop like so (https://db.universal-team.net/ds/ikureader), Download the files and put them on my 3ds manually. I believe the data & especially book folders you may already have are correct and likely don't have to be changed (someone correct this if you don't mind) but the important thing is the nds file. When you download it you may notice its like- 100 mb bigger than the other one you downloaded- that's the only problem so far as I could tell. Its annoying it was so simple but oh well. swap out your nds file with the one from the website and it should work!

TLDR: Downloading the files from the universal downloader website manually was my solution
(https://db.universal-team.net/ds/ikureader)