[RPG] Does the magus’ pool strike count as a touch spell

No, he can try again with his weapon melee attack. Per spellstrike,

At 2nd level, whenever a magus casts a spell with a range of “touch” from the magus spell list, he can deliver the spell through any weapon he is wielding as part of a melee attack. Instead of the free melee touch attack normally allowed to deliver the spell, a magus can make one free melee attack with his weapon (at his highest base attack bonus) as part of casting this spell. If successful, this melee attack deals its normal damage as well as the effects of the spell. If the magus makes this attack in concert with spell combat, this melee attack takes all the penalties accrued by spell combat melee attacks. This attack uses the weapon’s critical range (20, 19–20, or 18–20 and modified by the keen weapon property or similar effects), but the spell effect only deals ×2 damage on a successful critical hit, while the weapon damage uses its own critical modifier.

There are two separate clauses here - "he can deliver the spell through any weapon he is wielding as part of a melee attack" and "Instead of the free melee touch attack normally allowed to deliver the spell, a magus can make one free melee attack with his weapon." It seems to me that if the attack misses, the charge is held (just like if you were to miss with a touch attack on the same spell, it would be held) and you can try again with your own attacks, just like with normal spell touch attacks. The statement about the freebie doesn't say it's your only chance, in fact it takes pains to make it parallel with the usual free touch attack.

When you have the Ranged Spellstrike class feature AND the Pool Ray Arcana, it allows you to treat the Pool Ray as a completely different ranged attack with its own attack roll and damage.

So on one attack you have your Ranged spellstrike which deals your ranged damage plus the effect of your ranged spell, and you also have a free action ray that you get by spending one point from your spell pool that can either target the same target or any other target. In short it's extra damage on the target you're hitting, or you can target something else with it as well.

As for the latter part, for any ranged spell that gains more rays as it levels up, such as Scorching ray or Magic missile, each individual ranged attack during that full-round action has an accompanying missile, or ray that travels along with it. If you have four magic missiles but only three attacks, the last magic missile is wasted.