Ok, I fixed the issue where Realistic leveling was getting the wrong health on reloading. Now when you reload a save the current minutes drain effect is removed, and the spells magnitude is reset. Then the next drain effect is added (unless you were in the last minute when you saved, in that case all drain effects are removed).
So that issue and the issue using sleep/wait, or fast travel, should be corrected now.
As far as CM Partners having the wrong health, as I stated above it's an issue that should fix itself the next time the partners On Load block is run (the next time you see the loading message when using a load door, or fast travel) providing that the drain effect is no longer active on the player. What happens is when the drain is applied to a CM the effect is what we expect, but if the companions on load block runs things get messed up, here's my observations...
Before Resurrect CM > Base Health == 82 Current Health == 82
Resurrect CM > Base Health == 82 Current Health == 41
Move through a load door causing the loading screen to display > Base Health == 43 Current Health == 2
After resurrection things are as we expect them to be, the companion has their health drained by 1/2
When the companions on load runs it uses "getbaseav health" on the player, which doesn't get the players "real" base health because it doesn't check for active effects. In this case my base health would have reported 58 so CM does 58 * .75 and sets the companions health to 43. Since the CM now has a drain effect of 41 its current health is 2...It will recover about 8 health every minute now to arrive back at 43 when the resurrection effect ends. Going through any load doors during this time will change things again. Once the drain effect ends, going through the next load door will set the CM back to their proper health (according to what the CM mod thinks that should be, which is .75% of the players base health) providing the player has no other active health effects.
So you can see what we are up against here I hope. There are a few options none of which are perfect.
One would be to remove the drain of the partner completely, and only have the drain effect on the player. This would result in CM health being un-effected until you went through a load door, in which case the CM would have a similar drain to the players, but this would not be corrected until the next load door...
Two would be to rework the CM PartnerScript to check for active effects on the player when the onload block runs. This would be the best option, and is probably how it should have been done in the first place, but it's not something I really want to do.
Three I don't know lol. This is why I use a level offset of 10 on companions, so that they have higher health without having to go through extra scripting, which in the case of CM really doesn't work properly.
Anyway that's what I have for now. I suggest, when resurrecting a CM, take time to recover before charging through the nearest load door.