What
Instead of the well rested perk healing you completely, it now restores an arbitrary percentage of hit points which is fully configurable in the config file in the config folder. Sleeping will never heal you more or less than that percentage. By default your limbs are not healed but you are completely free to specify a limb condition percent to heal up to in the config file. You can also specify if completely broken limbs can be healed. I made this determination after considering a bleeding knuckle doesn't always constitute a doctor's visit but a broken arm does as it won't heal itself.
Why
Should be pretty obvious by now I'm a hardcore masochist, so I've been building tweak mods for a while now. Something that does this is oddly lacking. There is a mod that completely disables healing but I don't know if every player wanted to be so rough on themselves. The default percent of 33% felt appropriate and limbs should definitely not auto-magically mend. But with the ability to configure this mod to do more or less exactly what you want, it doesn't matter what I think would be appropriate since you can just set it yourselves to your tastes.
How
We edit exactly one script in order to replace a ResetHealth call with our own logic. Ini files are read when the well rested effect is applied. So this mod literally has just a script. Sadly this required an ESP plugin any way I sliced it. This was a necessary evil.
Installation/Incompatibilities
This works only in hardcore/survival mode. In normal mode, you heal and get the bonus wherever you sleep, it doesn't rely on the script we overwrite.

Anything that replaces or edits this script or does something to the perk that removes the script or anything up stream will be incompatible. For best results, add this mod as low in your load order as it'll go.

Settings are explained as following:

• fLimbRestoreCapPercent: To what percent sleep can restore a limb before it's left as is. 0 is never heal. 1.0 is heal to full.
• fHealthRestoreCapPercent: To what percent sleep can restore health before it's left as is. 0 is never heal. 1.0 is heal to full.
• fPercentToRestorePerSleptHour: What percent of your hit points or limb health will be healed per 1 hour of sleep. 0 is never heal 1.0 is heal completely within one hour. Don't worry, healing is cut off at the CapPercent values above.
• bFixBrokenLimbs: if a limb is completely broken, whether to heal it or not with sleep. At 0 broken limbs must be treated. At 1, broken limbs will heal when sleeping. Limbs that aren't yet crippled will not be affected by this setting.
• bNeedsEffectsRestoreRate: Determines whether to take your needs into account when calculating how much to heal you up. At 1, needs are taken into account. At 0, needs are ignored.
• bNeedsWellRestedMin: If your CumulativeNeedsPercent is ever more than this minimum, than you will not get the Well Rested bonus at all. You will still heal though. For how CumulativeNeedsPercent is calculated, look below. 0 is never give the well rested bonus. 0.5 is give the rested bonus when the player's CumulativeNeedsPercent is less than 50%. 1.0 is always give the bonus.
  

The formula for calculating how needs affects how much you'll recover is simple. We take into account your hydration, radiation and starvation. Then we check what percent those cumulative values are of 3000 (since each stat has a cap of 1000). That percent is then your CumulativeNeedsPercent.

At 100 radiation, hunger and thirst, you lose 10% of what you would normally heal.

TotalHealthToRestore - (TotalHealthToRestore * CumulativeNeedsPercent)
Requirements
1. xNVSE
2. JIP LN NVSE
3. Johnny Guitar