CapnScurvy is the man with the plan for the LAA utility with his
TEC - Win10 LAA SH4 Install thread. Full of all of the correct information. In Rockin Robbins package should be a really nice PDF file and he's got all sorts of good info in there. His MultiSH is the newer version, but I'm not sure of the LAA he's got in there. Be governed by CapnScuvy's advice on that. I can't say enough good though about RR's package. That SH4CMS can really save you a lot of time and aggravation, even what you just went through, just by using his utility. You do have to use a brand new, un-played install of the game though.
As for the mods, there is no bickering there. Bleiente has a new version of his Mod Soup (that IS the name of his mod
) and it is a good mix. He was just worried that you'd think it was his mod that caused your trouble. However, I'm like 99.99% it was what I refer to as Cross-Contamination, where after you deactivate a mod, then replay the game, the game pulls it's configuration information from that old save folder, and does literally cross-contaminate your new install. In Rockin Robbins package should be a really nice PDF file and he's got all sorts of good info in there.
Glad you're going now at 100%, now go out there and "Happy Hunting"!