An investigator adds her level to Craft (Alchemy) checks when making an alchemical substance (which I can't do anyway in PFS). An investigator can also use Craft (Alchemy) to identify potions, but the bonus does not apply, if I read the rule correctly. Have I the misfortune to be correct?
you are indeed correct. The bonus only applies to creating alchemical items.
It also appears that I can copy formulas from a wizard's spellbook, but not from scrolls.
An investigator can also add formulae to his book just like a wizard adds spells to his spellbook, <...>. An investigator can study a wizard's spellbook to learn any formula that is equivalent to a spell the spellbook contains. A wizard, however, cannot learn spells from a formula book.
As a wizard can add spells to his spellbook using scrolls, I'd argue an investigator can do the same. While I can see how someone could argue that as the later sentence only mentions spellbooks that's a limiting factor, but I read that later sentence as clarifying that it's a one way street with spellbooks rather than one excluding scrolls.
An investigator adds her level to Craft (Alchemy) checks when making an alchemical substance (which I can't do anyway in PFS).
Are you saying an investigator can't craft alchemical items in PFS?