After 3 weeks of testing this is what I have come up with.
When your pip-boy is saying something is wrong with a settlements water/food/beds are less than what they are you need to check your settlements for:
1. TV's, if any you need to scrap them.
2. Jukebox, if any you need to scrap them.
3. Beds, All beds must have the left hand side able to be walked up to or settlers will not be able to use them.
Its better if beds can be walked around on all 4 sides. (Sometimes it takes the cleanest looking bed and not a mod bed to fix it.)
4. Jobs, Any settler you assign to a job you must also assign them to a bed. Somehow when assigning a job to a settler will break there assign bed and they think they don't have one any more. This goes for guard post guards, you must assign them a bed after you assign them there job even when they will never use it.
So far after doing all of the above for the last 2 weeks of play all my numbers are matching up and they never complain anymore.
Happiness for all settlements now is over 80% all the time unless there about to be attacked then a red arrow will show and I just need to wait there until the attack or a settler will tell me they need help on something. (Do not leave the settlement until one or the other happens. Doing so may break it and the red arrow will stay around until another attack/quest happens for that settlement.)