The series 2 is a somewhat more "modern" wiring harness, quite different. For starters it has 4 fuses, with multiple circuits running up the spine frame where the S1 just runs 1 active up there and deals with it all in the headlight. I've not worked on many S1's but IIRC one fuse runs the brake light, the other runs everything else, which is not a great design really. The S1 harness is much smaller and thus neater where it runs up the spine. Like many I had nightmares when I saw photos of the mess in the headlight, but when I was working on Eddie's 1200 I grew some respect of it, it's not a bad system at all other than being a bit crowded in there. Eddie's bike started out more corroded than any bike I've ever seen (UK import) and although I had to re-terminate most of the wires to get rid of corrosion, it was all in surprisingly good order given the condition of the bike. I started out figuring I would rewire it with plugs etc as per the OP but after some familiarisation I came to realise there was little point as the system is solid if things are in good order.
The main failing of the S1 harness in my view (and actually I think it's the same for all) is that there is no earth wire going into the headlight, they rely on earthing through the steering head bearings/frame. I threaded a good earth wire from the main earthing point to the new coil bracket/frame and then on up into the headlight to earth everything properly in there. Well worth doing on any bike that does not have it already, will solve many weird problems.