Lemme see if I can answer your questions.
Gel Packs probably count as armor modifications, same as helmets and shields. Thus, they're kinda useless for low-STR characters, but their drawback would make putting it on one a bad idea anyways.
I'm certain standard upgrades do not take up slots; looking at weapon stats and comparing them with that in mind makes a lot of otherwise pointless options make sense (like "why does this gun with a smartgun cost more than this other equal gun and a smartgun accessory?).
Adding an additional shock pad would do nothing; there's no reason to think they would stack with eachother. Also, funnily enough, the chart on page 53 actually specifies that a shock pad does not stack with itself. So there you go.
They explain the initiative transfer more clearly in Level III P-Tac. The team leader can transfer from themselves to any other member. There's no rules about what action that is or when it happens, but it's implied it can be done once per turn (again based on Level III's rules) and I'd say it's probably done when initiative is rolled as a non-action.
Martial Arts specializations are more like Qualities. 7 Karma to learn an art, 4 karma to learn another technique. Spending skillpoints on them would have to be a houserule, and honestly, a rip off. 7 Karma is the same price a specialization, but after that, you're much better off increasing a skill beyond 2 (because at that point it costs more than 4 Karma to do that).