As I recall, Shinra only exposed their elite squads to Mako. They don't have the capital to waste on people who haven't proven themselves; doing so isn't good business. Cloud must have done something right, or he quite simply wouldn't have the power to face down Sephiroth; no unenhanced human could do what he did and live. Cases of "Mako poisoning" are mentioned, though. In the case of Cloud's time sitting in a wheelchair in Mideel, his mind had been particularly broken. It seems likely that Mako injection affects the mind.

Nowhere is it mentioned in the AC prologue or anywhere else in the movie where the characters are in terms of in-game mechanics. For all we know they could still be at Level 1, though this seems exceptionally unlikely.

Data in SE official publications is only valid when it does not contradict its source material. This applies regardless of what universe you're working in.