It's important to keep in mind that Ki Healing cares about Damage and not Missing HP. That means you have to do some mental (or physical) book keeping to track damage (and sometimes multiple damage types, if you're adding in the complications of Life Sacrifice). You also have to come up with the relationship between Damage and Missing HP. The short version of this is going to be: Track each damage source independently, and track how much and what kind of healing you've applied to each damage source.
Before we get into the details, I'm going to give my standard Anima disclaimer:
1.) The rules for this game are vague and contradictory at times. Not every example is guaranteed to have a good answer that is well-covered by the rules, and you may be able to cherry pick rules which result in a contradiction. Specific vs General is only of a small amount of help in many of these cases.
2.) I only know the rules in English, so anything could be wrong due to the (many) translation errors.
Now, on to your examples:
Imagine that instead of removing HP from a character when that character takes damage, you instead add a new value to your sheet called Damage. To check your current HP you simply calculate MHP - Sum(Current Damage values). Each time you take a source of Damage you add it to your sheet as a new value with an Original value (equal to the amount taken) and a Current value (starting at the amount taken, reduced by healing), and you add up the Current value all sources of Damage on your sheet to calculate your current HP.
When you Heal damage, you reduce the Current value of any number of Damage instances by a total amount equal to the Heal value. If any instance of Damage reaches a Current value of 0, you immediately remove that instance of damage from your sheet. For example: if I have 1 source of damage with both an Original and Current value of 10 and I Heal 10, I can reduce the Current value to 0 and remove that Damage from my sheet. If I have 2 instances of 10 each and heal the same amount, I can reduce either or both instances in any ratio (10 from one, 0 from another, 5 from each, 8:2, 4:6, etc..). This should pretty clearly work out to the "normal" way that one deals with damage and healing in Anima (and other RPGs). It's more legwork, but you can skip that extra work 90% of the time without a lot of hassle, or just deal with it in your head.
Now let's add Ki Healing into the equation. In order to track Ki Healing appropriately, we need to add another value to our Damage instance. Let's call this value Ki Healed. Each time you Heal Damage using Ki Healing, you must add an amount to the Ki Healed value of the Damage instance equal to the amount of damage Healed using Ki Healing. Any amount of Healing provided by Ki Healing which causes the Ki Healed stat to exceed .5 * Original cannot reduce the Current value as it normally would.
See (1), just calculate the percentage into a flat amount at cast time and then treat it as a flat heal
The limitations on Ki Healing are limits on Ki Healing, not on an individual source performing Ki Healing, thus you track Ki Healed an a damage source as a single value for all sources of Ki Healing.
See (1), treat each "tick" of regeneration as a single Heal and allocation the healing to damage sources as your please. Damage which is healed is removed, and further damage is treated as a new instance of Damage, which gets healing allocated to it independently.
As far as I know all Regeneration effects are combined into a single Regeneration value, natural, magical or otherwise. See (4). If there are ways to get two independent sources of Regenerations simply resolve their Heals independently as in (4).
This strongly depends on answers to your other question, so I will defer as I am not an expert on changes to MHP. I will say that at my table MHP increases always increased your current HP at my table (leaving nothing to heal) and MHP decreases took off equivalent current health, but I am not comfortable saying that our table played this "correctly". This does interpretation mesh nicely with (1) without requiring further changes (no new damage instances, no change to Original, Current or Ki Healed values).
I would have to consult the Life and Death section of the rules to say for sure (fortunately I interacted sparingly with those rules while playing), but I am inclined to treat this as a normal Heal effect and apply (1).