Where there are rules available, they’re found in the lycanthropes as characters section. A few of the questions simply don’t have answers in the rules, though.
You’ve misunderstood how lycanthrope skills work; a lycanthrope does not just get the animal’s ranks directly added to their own skills. Instead, they gain animal RHD, and they should get the skill points entitled to them for having those RHD, including their Intelligence score.
Racial Skills: A lycanthrope adds skill points for its animal Hit Dice much as if it had multiclassed into the animal type. It gains skill points equal to (2 + Int modifier, minimum 1) per Hit Die of the animal form. Any skills that appear in the animal’s description are treated as class skills for the lycanthrope’s animal levels. The lycanthrope’s maximum skill ranks are equal to its animal form Hit Dice + its racial Hit Dice (if any) + its class levels + 3. Any racial skill adjustments of the lycanthrope’s base race and its animal form (but not conditional adjustments) are added to its skill modifiers in any form.
So for example, if a wizard with Intelligence 18 became a werewolf, they gain two animal-type hit dice, which each come with 2+Int skill points, so 12 total for this wizard, and treats Control Shape, Handle Animal, Hide, Listen, Move Silently, Spot, and Survival as class skills for those two levels (any lycanthrope also gets Control Shape as a class skill regardless of class, and that applies to these two levels as well). The wizard may assign those skill points to skills as they like, per the usual rules for assigning skill points.
Retraining works on the skill ranks that the wizard assigned their lycanthrope HDs’ skill points to the same as for any other level’s skill ranks.
No, nothing about being a familiar shares the curse of lycanthropy, nor does anything about lycanthropy do anything to familiars.
The familiar would, as always, be loyal to the wizard. What that means for the familiar in question may vary depending on the familiar’s own thoughts and opinions.
If the familiar is in a pocket that melds into the lycanthrope wizard, I see no particular reason the familiar should take damage; I would just rule that the familiar winds up on the floor under the lycanthrope, or in the air above them, depending on the type of familiar. I don’t believe the rules explicitly handle this case, however.
I am not aware of any such list, and find it pretty unlikely that one exists.
A lycanthrope spellcaster cannot cast spells with verbal, somatic, or material components while in animal form, or spells with verbal components while in hybrid form.
So some spells, yes, but not most of them. Control Shape doesn’t come into play. Natural Spell only applies to wild shape, and not to other sources of alternate form abilities, though as DM I might be inclined to offer it to a lycanthrope wizard; they’ll probably need it.
Rules as written, no. Wild shape is a type of alternate form, and lycanthropy offers another type of alternate form, but Natural Spell requires the specific type of alternate form offered by wild shape, not just any alternate form ability. As I said, I’d probably consider it for a houserule considering all the problems that a lycanthrope wizard is likely to take.
Which, to conclude, let me just state that lycanthropy is really bad for a wizard. An afflicted lycanthrope loses four levels’ worth of wizard spellcasting progression, and a natural lycanthrope loses five. That’s a colossal blow to the wizard’s spellcasting, something that basically nothing in the game can actually justify, and lycanthrope offers almost nothing of value to a wizard. Even if allowed to take Natural Spell, that’s another feat on top of the four or five levels of lost opportunity just to be able to use alternate forms that don’t benefit you very much. And if not allowed to take Natural Spell, you get very nearly nothing for your trouble.