I'll take a crack at this, since no one else has...
Cloak of the Manta Ray is a leather cloak in air or non-salt water. So the second a person would leave, they would then be back to normal.
Assuming the person wanted to maintain that state...
Life bubble would continue a artificial-magical saltwater environment, I think. I would require it to be cast while in the manta ray form, however, as it would maintain their requirement for living at the time of casting. Arguably, it could adapt as they exited the water, but I'm assuming you're looking for justification. After all, I'd assume there's easier ways to be a flying mount Now all of this wouldn't allow them to swim through the air.
Which is where you went with sky swim. Yeah, they can now fly using their swim speed. However, it only lasts a minute per level. Not very long.
As far as the now flying manta ray being a mount, I would say virtually anything can be used as a mount, but aren't trained as such. D20pfsrd does talk about a manta ray as a viable aquatic mount, although I can't find it stating that in the books. It is a viable animal companion, so doesn't strike me as unreasonable anyway. In this case, it sounds like you're making a PC a mount. I don't even know what the complications of that is, suffice to say aplenty.
From this point on, I can't really find much in terms of rules. Riding a mount usually involves the rider controlling the mount via ride checks. A player character as a mount has their own mindset and actions. That's no different than a regular mount, but we tend to ignore the mount as a separate entity because the rider controls them.
In play, I'd give the manta ray player the benefit of assuming he's "combat trained". Fighting with a combat-trained mount is a ride DC of 10. But the magus isn't riding a normal mount, and they're riding a flying mount. I seem to remember a +5 from 3.5 for exotic mounts. Can't find that in Pathfinder, so you could waive it. A mount flying doesn't seem unreasonable to raise the checks by +5. This is comparable to making a mount jump anyway, which is DC 15. Might actually even be a +10, but I lean towards +5.
I would make the Magus make a DC 20 Ride check every round he's in combat (as a free action). If he fails, he is unable to act this round. If he fails fantastically, he falls off the mount. Anytime he wants to cast, he has to make a he needs to make a concentration check (vigorous motion being 10+spell level, and frankly, a mount in combat probably becomes violent motion making it 15+spell level). I'd probably make there be an option for an exotic saddle that "straps" the wearer in preventing falling from the mount, but in turn, I'd make it a full round action to mount/dismount.
No matter the intelligence, if you're riding something you use mounted combat rules. Unless you have the Mounted Skirmisher feat, you aren't making a full attack when your mount moves (more than 5 ft). Regardless of whether the mount is a sentient being polymorphed into something else or not.
If a character is being carried by another character, even if not riding on it's back, it should probably be treated as though it were mounted.
At the very least, there is no way that you should get a full attack while moving (or being moved) unless you have pounce or some other special ability that allows it.
You're not missing anything EvilMinion, that's why I was pointed it out as well.