1) Prep penalty is applied per unit and not per stack of units, and mainly applies to amphibious invasions. This seems to indicate prep does not play a role in non-amphibious combat, so if I really need to invade Rabaul in a hurry it would seem I could invade an unoccupied hex nearby and march to the target (erm.. not sure I can do that). This also seems to indicate prep doesn't need to be closely managed for static land warfare in Asia.
Preparation of BOTH sides influence combat. Just NOT in serious way (it seems defender gets penalty, when NOT 100% prepared). Also, preparation of COMMANDING HQs influence combat, in serious quantity.
You can prepare to land ONLY against bases. You do NOT get assault landing ONLY in friendly base. If there is NO base in hex, landing will be ALWAYS unprepared. That means around 50% squads disrupted/destroyed, when you unload out of base.
2) Units prep faster in rest mode
I am not sure, but probably not.
3) If sub-units are re-combined, the larger unit is prepped based on the prep target of the sub-unit selected to perform the re-combination.
Also percentage is averaged out. If one unit was prepared at 100%, and second at 50%, whole unit will be around 75% after recombine.
4) Units will train as long as a target is prepped to 100. It does not have to be a specific target and this calculation is separate from lack-of-prep disruptions that would occur as part of an invasion. So, prep probably does not need to be managed for non-combat units such as base engineers (May be better for that unit on Wake Island to have San Francisco at 100 and be training, than lose the time to prep to current target), but units that will "fight" in an amphib invasion (Inf, Armor, Art, CD, Combat Engineers) should prep. A HQ then becomes an unknown if it is not in the same hex.
There is maximum exp level, depending of nationality. Mostly around 50. Then, they will get exp only by combat. And during defending, your SUPPORT SQUADS, also add 1/10th AV for combat, so all units should be prepared for hex.
5) Preparation applies to defending units (but fortification is unrelated). On the surface this seems to contradict #1, unless it is only a factor in defending against amphibious invasion.
It probably also reduce damage from air, and sea attacks. AIR HQ prepared for enemy base causes more planes to fly against it.