The mechanics were all non-commissoned officers in the Confederation Navy. The manual for Prophecy says that Rachel is a Master Chief Petty Officer, Pliers would most likely have been that rank as well (given his age) and Sparks was a Chief Petty Officer (it said so in the dialogue). Chief Technician was probably a position rather than a rank, like Commander Air Group or Wing Commander although that's taken from an actual officer rank in the Royal Air Force. As a matter of matter Chief Technician is also an RAF NCO rank, equivalent to Staff Sergeant in the British Army. But the RAF/Royal Navy equivalent of a US Navy Master Chief is Warrant Officer.
Your insticts are correct--the Wing Commander IV novelization confirms that Pliers was a Master Chief Petty Officer (or at least he retired from the Confederation as an MCPO).
I will also point out that Sparks actually finished the war as a commissioned officer, following her service with the Landreich... which left her an odd duck in the postwar military. I mention that only because it ties in to something below...)
While on the subject of ranks in Wing Commander, I think various characters in the games had the wrong rank. In Prophecy Hawk was a Colonel but didn't seem to be in charge of anyone, whereas the CAG was in charge of all the pilots and she was a Navy Commander (which is below Colonel). Also in WC4 Panther was far too young to be a Colonel and exactly seem to have the job of one either. I don't think full Colonels (or Captains) actually fly in real life, they're too high up. And Vagabond was one of the oldest pilots but he was only a Lieutenant. Lieutenant is not a rank officers tend to spend very long in. In WC3 I think at least Vagabond, Flint and Flash (way too young to be a Major) should have been Captains, but then I suppose they thought people would get confused and think they were on the same level as Eisen. In fact why was there a Space Force and a Navy when the pilots all flew off the ships, which makes them more like Naval Aviators. I suppose they rectified this in the film, pile of crap though it was.
I believe it's normal for Lieutenant Colonels to fly in the USAF--they're the squadron commanders (and as in Wing Commander, Colonels have the option of flying or not... it's only general officers who are specifically barred). Captains certainly fly (I believe we have at least one who posts to these forums, even...).
The issue here isn't that they have the wrong rank, though, it's that their ranks are a result of the war. Our peacetime ticket-punching promotion system didn't apply for years and years--instead there was a system of merit-based promotions designed to move those precious few pilots capable of surviving months or years of combat into command roles as quickly as possible. That's what leads to Blair as a Colonel preparing to take a Wing Commander's slot at age 26... and all the other, lesser things.
Everything changes after the war and we see it discussed in the novels. You suddenly have a top-heavy military with no place for new recuirts--who are no longer dying by the hundreds--to advance. In Wing Commander IV the military is just starting to begin that transition (think of the reduction in force after World War II, with new rules established to eliminate all sorts of people who made great soldiers during a war but who didn't necessarily have the qualifications to stay during peacetime.)
The ranks in Wing Commander III were all chosen to explain something about the character. Remember that Vagabond is supposed to have a dark past and eventually reveals he had worked on the Temblor Bomb with Dr. Severin. The idea was that he had seen terrible things and then had trouble adjusting to the military--to the point that he's been unable to stay in one place (until he gets to the Victory). That's why he's older and just a Lieutenant. Flash, on the other hand, is supposed to be a favorite son and the inflated rank is supposed to express that. He answers directly to Tolwyn and so forth in the game. (The book further explains that the rank comes from the fact that his father funded the Home Defense squadron that gave him his commission in the first place.)
We don't know Panther's actual age, but we do know she's a veteran of some note ("I know those names" - Blair), so it would make sense for her to have a higher rank. Her job description certainly fit the rank, though--she was a fighting squadron commander, the Intrepid's acting Damage Control Officer and (later in the game) Admiral Wilford's staff operations officer. (Also, note that her rank is with the UBW under very unique circumstances. She was an early recruit for the Union of Border Worlds, who were desparate for leadership... the fact that they commissioned her as a Lieutenant Colonel during their founding crisis doesn't mean that's what she left the Confederation as.)
I don't think it's clear exactly what Hawk's responsibility is on the Midway... because none of the assignments are very clear. I had always assumed he was there to take command of the elite 'third' wing when it was delivered--but it's also possible he's some sort of staff officer (he's flying with the Black Widows early on and may be their Wing Commander until Maniac is given that position). (Note also that he's some sort of exchange officer--transferred over from the Outerworlds Fleet at Blair's personal request.)