Thats as succinct as I can put it... I dont know what the problem is, but im running a largely unpatched game and its likely the cause of a number of buggy things im seeing, or rather, not seeing...

I use LOOT and WRYE BASH every single time I do anything to my system, dont know why it wont accept them...

I have not used Loot in quite a while since I have not played Skyrim for quite some time. Loot should be telling you something about the load order as well as Wyre Bash should be telling you if you have a missing master since most of the crashes at startup are due to either a missing master or wrong load order. If using Loot you should not be having an issue with the load order since as far as I know it checks what masters each mod needs.

[edit]

When you add/remove/update a mod did you make a new bashed patch.

Every, single, time...

the things in the bashed patch might have changed with one of your changes so the bashed patch might have incorrect information and could cause issues.