The reason things are worded so badly lies in the 3.0->3.5->PF transition. See below for that! I believe chill touch is still resolvable using the RAW, though.
Chill Touch
The answer to the chill touch question lies in the rules for holding the charge:
Touch Spells and Holding the Charge: In most cases, if you don't discharge a touch spell on the round you cast it, you can hold the charge (postpone the discharge of the spell) indefinitely. You can make touch attacks round after round until the spell is discharged. If you cast another spell, the touch spell dissipates.
Most touch spells discharge after a single successful attack, but chill touch makes it clear that this isn't the case. Instead, you get one touch per level. So the quoted rule allows chill touch to be used across multiple rounds; there's no need for the spell to explicitly state it. (Though it probably should, just for clarity.)
Willing targets
The rules do explicitly state that you can't hold the charge on multiple targets, so no help there! That seems to be the simplest solution, though.
As an aside, an effect that changes the range of touch spells would "unlock" the full number of targets, so there is a technical difference between the current state and your alternate wording. :P
A little bit of history
So why are the RAW in this state? Well, I did a bit of digging, and this thread was very helpful, especially this post by Hypersmurf. (Who I remember from when I posted in the enworld rules forum far too often -- thanks Hypersmurf!)
In 3.0, you could touch 6 willing targets as a full round action, or one as a standard. There was no restriction on touching all the targets the round the spell finished -- in this context the 6 target limit played well with multi-target spells.
In 3.5, the Magic Overview section was changed: the limit of 6 was removed, but the requirement of touching the targets in a single round was added. However, the rules for touch spells in combat left the old restriction of 6 targets in place. The text here directly contradicted that of the overview section. If you assume that the wording of the overview section was what the designers intended, this would still cause no problems with touch spells targeting multiple willing creatures.
In PF, both limitations are included in the overview. I would assume that someone was trying to reconcile the contradiction mentioned in 2, without realizing that it was a holdover from an intended 3.0->3.5 shift. The result? Accidental nerfing of multi-target touch range buffs.
Likewise, the wording of chill touch has been essentially unchanged since 3.0. It's been edited a little to make the wording less clumsy, but not updated to account for the changing touch attack rules. This explains why it doesn't explicitly call out that it carries across multiple rounds.
As I see it, there are two basic parts to this question: can you hold the charge on a Reach spell, and is the 'ray' made by a Reach spell visible?
To the first question: You cannot hold the charge on a Reach spell. A Reach spell is a ranged touch attack, and the rules for holding the charge specifically call out touch attacks, which are different. The relevant rules are:
Touch
You must touch a creature or object to affect it. A touch spell
that deals damage can score a critical hit just as a weapon can. A
touch spell threatens a critical hit on a natural roll of 20 and deals
double damage on a successful critical hit. Some touch spells allow
you to touch multiple targets. You can touch as many willing targets
as you can reach as part of the casting, but all targets of the spell
must be touched in the same round that you finish casting the spell.
Touch Spells and Holding the Charge:
In most cases, if you don’t discharge a touch spell on the round you cast it, you can hold the charge (postpone the discharge of the spell) indefinitely. You can make touch attacks round after round. If you cast another spell, the touch spell dissipates.
Since that passage only mentions touch spells, and not ranged touch spells, you cannot hold the charge on a Reach spell.
To the second question: Whether or not you can stealthily cast a Reach spell is pretty much entirely up to your GM. The description of Reach Spell says that the affected spell "effectively becomes a ray", which says to me that for all intents and purposes, you treat the spell like a ray.
The fact that it says "effectively becomes a ray" and not "becomes a ray" is a semantic difference that has no real meaning. There are no exclusions listed for why it says one and not the other, so it's likely that whatever designer wrote this feat liked the sound of "effectively" more than not, and his/her editor agreed. Since the feat doesn't list any ways that the spell doesn't work like a ray, it's a reasonable assumption that it always works like a ray.
If your GM says that Reach Spell rays are visible, then they are. The rules aren't terribly clear on whether rays in general are visible, but clues from flavour text and descriptions strongly imply that ray spells are visible to normal vision, and thus can be seen by anyone who is looking.
Best Answer
No, touching an ally does not provoke AoO.
Pathfinder SRD, Combat (emphasis mine):
Armed melee attacks do not provoke an AoO.
This is explicitly repeated in Touch spells in combat section:
The exception to this is a full-round action to touch 6 allies, which always provokes an AoO.