1) Shield Mastery. Maybe a little unbalancing? A 3rd Lv Soldier with fighter as specialty can easily negate up to 6 points of both AP and Keen. If heavy armoured this soldier can't be damaged by most weapons ... and is only a 3rd level...
While AP 2-4 is pretty much the standard/average of what any weapon can and will probably have (upgrades after all), Shield mastery mostly just allows someone to actually make use of their armor. To me it feels more like "without this, there's no point in bothering with light and most moderate armor". Better off with cheap cloth loaded up on resistances.
Throw in shield mastery however and all of a sudden your armor's useful again against anything short of AP bows and crossbows, but that's what heavy crossbows are MADE for.
Several damage types ignore DR entirely. Stress, electrical, sonic, flash... You can also try to disarm or destroy the shield itself, depending on what you have available. Take a moment to rid him of his shield and you've just invalidated the ability, dropped his guard bonus, and neutralized several tricks. A shield can and SHOULD make someone a pretty tough nut to crack, as that was exactly what they did in reality.
2) About the called shot trick.
I'd suggest no. While going around light armor probably should be doable that easily, learning to slip between plates and 'go for the visor' reliably takes more than a little bit of practice, something not everyone might learn. DR seems easy enough to bypass, neutralize or reduce as it is, to be honest.
3) I do not like the idea of having mages as healers so I ruled, using the Sorcery -- Lost Magic (Healing), that the school is not available to them. (Reputation can not be used to access the discipline)... I've nothing against magical healing, just I do not want the mages to handle it... so, how to reintroduce it?
The problem here is that a "healer" type cleric of the D&D healbot kind IS pretty much a mage in Fantasy Craft. The armor restriction isn't there in this game, so the closest thing to a proper "cleric" is one or two levels of cleric for the "domain" and rest all in mage.
However, the 'wizards' are nowhere near as powerful, invulnerable or practically-infinite (by 15 or so, if it would be enough to run the wizard out of his prepared spells, its killed the rest of the party twice over even if through just attrition) casting as they are in other games, so it shouldn't actually be as much of a worry. There's a fair amount of fluff/systems/settings where mages heal anyhow. You can easily get similar damage output from non-casters in FC, there's plenty of abilities and ways of getting the buffs and other special effects, and the casting requires rolls atop all this, giving a low, but non-zero chance of fumbles and casting-failures.
I get the feeling the spell compendium's new classes will have your answer though.
4) About the touch of light and the healing spells in general. How do you handle them? (I've seen another thread about that spell, maybe some new solution was developed since then)
Its inconsequential. Anyone can just wait, and not all that long, for their vitality to recover anyways. Touch of Light is a lot of work for very little gain: awesome for emergencies, but a party that uses it to its limit after every fight would be camping or otherwise trying to recover without it anyhow. Most don't really bother much.