All arcehtypes get talents and skills that some are aligned to a certain god. Are these starters counted towards alignment, when it is checked?

No, only advances bought with XP (including starting XP) count. That obviously means that when you have a choice between two things from your archetype (e.g. Parry and Dodge) and you want both, you choose the one that doesn't fit with your alignment and buy the other one with XP.

also: are each level of a skill considered a further alignment towards the god, or is all the levels from rank 1 to rank 4 only one advancement?

each time you buy skill, talent or stat advancement it counts towards a god, so getting dodge and dodge +10 nets you two points (for griffindor) towards slaanesh.

my players bomb me with questions that I can't answer… *sigh*

Can you choose the talents at the character creation without meeting the prerequisites? I'd think yes?

Yes, but only at creation. If they later want to buy talent they could have chosen, they have to meet prequisites.
It was cleared in rules clarification tread.

Can a character use xp to get infamy in order to change the multiplier, thus gaining 1 additional automatic item?

From Character Creation: Equipment and Corruption:
'The number of pieces of gear available at this stage is equal to the Heretic’s current Infamy bonus.'

Seeing as you choose equipment after you spend xp, yes he can.