Then you should have read what I said because I mentioned that I didn't have any other mods besides my own installed. I know that mods that alter breezehome crash the game but that is why this thread is here to find out exactly why.
I HAVE FOUND THE SOURCE OF CTD!!!!!
The internal non load doors in the house are the cause of the CTD! Each of the xmarkers I mentioned earlier have a door assigned to them. One door for housecarl room, one door for player bedroom, and one door for child room from hearthfires DLC. I tested this to confirm it does indeed crash when any one of those doors is set to just show up in the house aka not part of an upgrade package but there by default. Go into CK load update and hearthfires, go to breezehome and set any one of those WRdoor02 to none under enable parent and save it as a mod and then load that mod in the game. Use coc whiterunbreezehome command at the console to immediately go to inside of breezehome and notice the CTD right away! Now uncheck that mod and do the same things again and it loads just fine.
So far I have tried rotating the doors by one degree or more since they are all at zero or 90 thinking the game has a problem with absolutes on doors in HF but it still crashes. So it must be something else with the doors but THIS CONFIRMS it is the doors crashing the game not navmesh directly.
I am gonna try experimenting with replacing the doors or using different settings with the doors and see what happens.