What I did here was changed all of the TTWFunctions quest stages into User Defined NVSE Functions. I also changed the formID of both the Quest and it's associated Script so that any FUBAR saves would see it as a new quest and hopefully ignore all the old references to the old, messed up quest.
ANY mod that made use of SetStage TTWFunctions needs to now make use of the NVSE User Defined Functions I've implemented.
There are some hotfixes for use with this hotfix, that otherwise will not work correctly, find them here.
Difficult Journey: https://taleoftwowastelands.com/comment/47020#comment-47020
Start Up Menu: https://taleoftwowastelands.com/sites/default/files/RoyBatty/ttw_startupmenu.7z
Improved Transportalponder: https://taleoftwowastelands.com/sites/default/files/RoyBatty/ttw_transportalponder.7z