It looks like the omod isn't doing what it's supposed to be doing. I get a question about Real Lights, but not about which version of the esp I want, nor is it installing an esp for Shivering Isles. Only the "real lights" esp is installing. I strongly suspect this is what's causing the crashes since other esps are likely expected by the script.
edit: I'm also looking at the script and what's supposed to be installing. The only plugin installing is "All Natural - Real Lights.esp", no esms or options.
edit edit: It looks like you're missing an endif after the first question, so the rest of the entire script is falling under "else" and not executing if I answer "yes".