To pretty much sum up what everyone else on these forums is saying, re-installing over 130 mods is a mere child's play compared to the endless weeks/months of aggravation from not determining the problem child. TTW is fun and fixes up a TON of errors about the game. Think Mission Mojave on steroids (or NVEC, as I previously mentioned). That said, mod compatibility takes a... well, not necessarily a nose dive but it requires more attention.
It takes me about a week to get all my mods reinstalled and that's pussy-footing and taking my sweet time. A dedicated modder like yourself should have no problems getting them all reinstalled in a matter of a day or two at most. I've 114 items in my load order (more if you count the inactive ones for sake of memory). Consider the major game altering mods first to be looked at, like that alternate start mod. Then quest mods that tie into the background story, like FOOK 2 (F3 version). Finally, try posting a load order and we'll see if we can't figure out what's causing it. Still, if after disabling everything non-TTW isn't working, uninstall your mods and/or do a fresh TTW and FNV install (do the TTW install to an outside folder to make it quick and easy to reimplement). That's all the advice I (and we) can give.
but it still doesn't change the fact that it is still very early to be using mods with it, my advice is to always install mods one by one and like 
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