the 1S, 2S & 4S will most likely mean seconds (I have two 645's, a 1000s and a Pro TL, and the seconds are in a different colour I'm pretty sure, but I haven't noticed the 'S'... I should pay more attention!)
The mamiya site has some manuals in PDF format, however the 645E isn't included, and it sounds like you have the manufacturers manual anyway (and I agree they seem a bit light on detail... eg, I can't find what my prism finders metering scheme is and i'd like to know!)
As for processing your film, I would just process normally. If it was REAL important to you, and you don't already use one of the speed 'enhancing' developers then you could use one of them (eg XTOL) but that would mean you'd probably have to do a few tests to dial in a development time before doing the important roll.