Hey, I'm having this same problem as well. I also use sysmodules but I'm pretty sure they were disabled when I updated. However, I'm able to boot just fine after removing the contents folder. I thought maybe it had something to do with sys-clk's folder so I removed that and still nothing. I read that ppl were saying to delete 0100000000001000 but I don't have that folder.
edit: I'm currently moving the stuff I had in contents over one by one to see which one stops it from booting...
edit 2: So I found out, for me, it was folder 010000000000bd00. I'm unsure if this folder would've had the same contents as 0100000000001000 does, but removing that helped. I'm also not sure if the bd00 folder has stuff I actually need. Would it be fine to just leave it out for right now?