Update: Its been a few nights of playing, both in and out of the game world. There has been some sleep, but overall the sleep activating system still seems unstable with my load order.
Load order hasnt changed that much, but Ive updated Vigor from 8.0 to 10.2. Vigor is a candidate source for some part of this bug. Im still using the "Enable Wait" mod. At first there was no effect, but then, after a healing from the priest in Riverville, I tried to wait, and the menu fired. Mostly, but not entirely, Ive been able to sleep and wait since then.
The above mod seems to have helped.
In other news, now Im having trouble mining ore. Thats also an Activator bug...
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October 10, 2016 edit: the pickaxe in my inventory was not being detected, perhaps because it had been improved to 'Pickaxe (Superior)'. Once a [player.AddItem 000E3C16 1] pickaxe was added, I was able to mine again.
...Im wondering if it could be new textures causing some of these problems.