Okay guys thanks for all the comments
clodcosades: Yeah, turns out none of the dead pilgrims had health set to 0. Oops. Fixed in 6.1. And the weird spells isn't MCA. As for the hood, I renamed it _MCA_hood_niero. Hlaalu Agents wear them, so look around the Balmora council building I guess.
Tes96: Yep, I'll make a new patch as soon as NOM 3 is released.
Ronin49. Hey dude. I won't just yet.
Pwin: Checked all my leveled lists and thugs shouldn't spawn until level 3. You positive you were at level 1? And the main problem with 5.2 was that they all had enchanted claymores and hammers and stuff, but I got rid of all the 2 handed weapons from their weapon lists.
Raym: No, they weren't meant to be nvde. My bad.
And yeah, I screwed up the removing of the crosses. I put the replacement texture in the wrong directory so it didn't overwrite the old one. Duh. Again, fixed in 6.1.
Got a nasty case of flu last week and didn't even have the energy to sit at the computer, so 6.1 has been delayed for a few days. But it's progressing well. Just adding in some mini-quests for the Daedric companions (Arran, Zharna and Shareel) so there's a bit of a reason behind them agreeing to travel with you. Zharna's (the seducer) is all done, and I'm part way through Shareel's at the moment. Not long to go.