I had a similar situation yesterday: Installed MO 0.0.1 plus patch 2 together with a couple of additional favourite eye & ear candy mods. Made certain adjustements to options.py (from my earlier options.py). I had CTDs upon starting (or continuing) a (new) campaign even before getting into the bunker. Thought maybe the reason was a sloppily adjusted options.py.
Took a fresh (virgin) version of MO patch 2's options.py and, instead of applying earlier settings with the OptionsMigrator, I took a previously well working options.py with my favourite settings, and opened it together with the virgin options.py (from patch 2) in Winmerge. In Winmerge it was ever so easy to compare both file versions, to pinpoint the differences and thus to transfer my favourite settings. This way I made sure that the new adjusted options.py was clean from sloppy errors like possibly in the earlier CTD version. Indeed, with this 'new' options.py adjusted with Winmerge, there were no more CTDs, and all has worked well.
