Some of the ambiguity you are seeing is because monsters were not actually built using the Custom Class creation system. Instead, the transformation rules are more-or-less an emulator to let you convert between the two.
In another thread, I posted an example for orcs and bugbears of how you can create monsters that function exactly like Player Companion classes while also being 100% compatible with the transformation rules and the monster listings. I have since begun working on some expanded rules for monsters that will be published in the Lairs & Encounters supplement. For the time being, here are some responses extracted from this future effort:
- What happens with armor/weapon/fighting styles? My intuition says that the character can use any weapons/armor he used before transformation as well as any new natural attacks, but doesn’t gain any extra equipment proficiency. However, this is not 100% clear and since monster attack progression is equated somewhat to fighter 3 in custom class construction, I’m not sure (I assume they don’t automatically get the damage bonus). Furthermore, the character is supposed to lose all class abilities (iirc), so weapons/armor skills might qualify.
APM: If the character’s new form is substantially similar to his old form (e.g. a man into an orc), then he would retain the weapon, armor, and fighting styles he already knew how to use. If the character’s new form is substantially different (e.g. a man into a harpy), he would likely lose his existing training, as his new body would be so different. If he wishes to retain it, and it was anatomically viable, the Judge might allow it but apply an * to his XP curve.
- What happens to class/general proficiencies? It would seem odd for a mage to become worse at necromancy upon becoming a lich because he “forgot” Black Lore of Zahar.
APM: If the character’s new form is such that his mind is intact, he should retain his proficiencies. If his new form does not give him the means to carry out certain tasks, he may not be able to use the proficiencies, though he wouldn’t forget them. (For example, a hydra-man might not be able to pick locks with his huge claws).
- Does a transformed character learn new proficiencies? I would think that class proficiencies would be a no since they lost their class, but maybe general proficiencies still work.
APM: A monster with an Intelligence bonus will gain additional general proficiencies equal to this bonus. (This is unlikely to apply if the character’s INT didn’t change). When a monster acquires more HD than normal for its species, it earns additional class and general proficiencies; treat each HD gained as a class level gained of fighter. A monster also gains an additional general proficiency when it reaches the middle aged, old, and ancient age categories for its species. The Judge should determine what the monster’s class proficiencies are, and what its age categories are.
Native born monsters will possess the Monster proficiency (see below), but most transformed monsters will not.
Monster: The monster is well-equipped for life as a creature of its kind. The specific tasks which are covered by this proficiency are determined by the type of creature, but generally will include knowing how to find food, secure shelter, easily open stuck dungeon doors, etc. This is the equivalent of the Adventuring proficiency for monsters.
- What kind of guidelines are there to setting a new custom creature’s ac or natural armor? What, save the judge’s wrath and common decency, prevent my lich from having enchanted bones the strength of plate armor? Also, how does natural armor and physical armor stack, if at all?
Natural and physical armor stack, provided that the physical armor can be fit over the natural armor. If the result is an ungodly number, you might consider a less-high AC combined with some form of damage reduction (such as the mummy enjoys). That is definitely up to the Judge’s discretion.