First, I'm not sure how indirect touch spells are supposed to work. My understanding is that for most spells, you establish touch with an unarmed combat attack, using melee modifiers, including +2 for touch-only, you win grazes, and net hits don't matter. If you touch, you have a magical link, and you can make your spellcasting test against that target normally.
I'm not sure how that translates to indirect spells though. For those, you make the spellcasting test as a ranged attack. Does "touch" mean that you have to touch the target and make a ranged attack? To me it makes more sense to combine the two and make the spellcasting test as a melee attack. But then I'm not sure whether you should use the +2 touch-only modifier, or whether you should win grazes. My inclination is no, but I don't want to be overly harsh.
Related to this, I seem to recall that you can cast a spell through a weapon, but I don't see the rules for that, and it's not jumping out to me how you'd handle it.