Rob, there are no easy answers to the air and electric questions you have asked. As part of a restoration project that I'm working on, I have acquired quite a few representative electrical schematics (and more recently air brake drawings) and have studied them in great detail.
I'll try and keep this brief, and bear in mind that what I am speaking in general terms here; ABC RR's RS-3s may not have left Schenectady with the same equipment that XYZ-s RS-2s had. Railroads ordered different options in MU, air brake schedules and many other things.
Also, another good primer was published in Trains many years ago, called Lash 'em Up. I've found a few minor mistakes, I've never seen a FO/RE setup switch, for example.
Speaking as an electrician, the electric side is easier to start with. First, the BLWs GENERALLY (and remember that word-) had air throttles, as did some Limas and maybe some of the FMs. I'm not that up the air throttle units, so this will deal with Alcos, GEs and EMDs.
The MU connectors came in (at least) four sizes that I have seen; 12 pin on a 44 tonner, 19 pin on an Alco switcher or RS-1, 21 pin on some earlier road units, and the (AAR) standard for today, 27 pin. These have as a minimum, the four (or three on a 539 Alco) throttle control circuits, battery negative, positive control, generator field, forward, reverse, sand (if electric), wheel slip, alarm and fuel pump/engine run. (I know thats 14, I'm not sure what the 44T doesn't use-) I also think EMD used a 16 pin on early passenger power.
Sometimes an adaptor cable could be made to mate a 21 pin unit to a 27 pin unit, but 19 pin to anything else requires some serious electrical work in the 19 pin unit. I am familiar with a pair of Radio Control Cars that were used for mid-train helpers, they had a 21 pin connector up high, with high mounted connections for 6 air, and a low mounted 27 pin, with hoses for 24 or 26 air. These cars had to control both RS-3s and SD-40s, therefore they had two systems basically in parallel.
Mentioning the RCCs leads me into the air side; typically a switcher has 6 or 14 air, with three hoses: train line, main reservoir, and cylinder equalizing (or apply and release). On switchers, the two extra hoses, (MR and A/R) are under the coupler. On a road switcher with number 6, like many RS-2s and RS-3s, the hoses and MU connections were mounted up high, centered on the end handrail or on either side of the drop step.
As time went on, the 24 and 26 air brake schedules came out, and the MU shifted to 27 pin. (But not at the same time-) The three hoses for 24 or 26 (in addition to the train line) are MR, actuating (or bailoff, which releases the locomotive's brakes) and apply and release.
During the transition period, so to speak, between high and low mounted air and MU, some units were built that had both systems. Two examples come to mind. The L&HR C-420s had two hoses up high, to MU with their earlier RS-3s. Two hoses tells me that the RS-3s were 6 equipped; I'm not sure how many pins in the RS-3 MU, I've never seen a drawing. The Centuries also had MR, Act and A&R down low.
The GB&W had newer units (RS-11, RS-27s and Centuries) with both high 6 air and low 24 or 26 air, to run with their RS-2s and RS-3s, but the were all 21 pin until the Hornell units came in the early 1980s. At that time, the RS-2s were gone, the RS-3s had been rebuilt into RS-20s, so the higher connections came out and the units got drop steps.
As far as transition goes, many newer units were built with automatic transition, but had the lever in the control stand so the engineer could "shift" older trailing units manually; another two wires. Also, the current standard for sand is for electric sanding, but air sanding was in use for many years. One hose for forward, one for reverse.
Hope I've answered more questions than I've raised. I've rewired a few units, and brought them up to current MU standards. And remember that the above is in general terms, typical practise. There are always some exceptions, special orders or upgrades that railroads did to their own equipment. (I know of an Alco switcher with EMD controls and 27 pin MU, for example-)
