@Calum @raceraidan Interesting thread.
I once owned a 1998 DT125RE French import which looked identical to a DT125R the same year (pic 1). It had a larger battery and separate toolikt compartment as well as the electric start wiring.
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During this time I was fortunate enough to source a Yamaha service manual for this exact model, I still have this and here are some pictures of the wiring diagram. I believe KTM also used this engine/electrical platform for the LC2 125 which they sold a lot of in Germany (I bought 2 or 3 3MB CDI units marked LC2 125 from German breakers, and also some NIP 3MB YPVS servos which had both the Yamaha and KTM part numbers on the packaging (sadly now all sold). During my ownership I tried all these items on the bike and they all just plugged into the loom (same connectors) and worked. I'm pretty certain the (inverted) flywheel and stator were both stamped 3MB.
As you can see this model also has a clutch switch which IIRC, with the clutch pulled in, allows you to start the engine in gear even with the sidestand down, but cuts the ignition when you let out the clutch to try and pull away. If you've already looked at the sidestand switch I'd locate this and give it a dose of WD40 etc. as a starting point. Also the two relays (items 12 and 13) are worth a look although I'm not sure how you'd go about testing these.
It might be of some help to just get some more and plug them in and try them. Here's a link to the KTM parts fiche; search Google/eBay etc. for the KTM part numbers as well as Yamaha France and you might get lucky with a European breaker as they can be quite diligent with posting up used parts for sale including the original numbers:
https://www.trevorpopemotorcycles.co.uk/index.php?main_page=ktm_fiche_finder
https://ypec-sss.yamaha-motor.co.jp/ypec/ypec/b2c/html5/app/en_GB/parts-search/index.html?ver=bd30d8f2-88bf-45bf-81ba-b46167a61f3c
Here are some pics of the wiring diagram, not sure if the Gilera SC125 used the same electrical platform but hope this helps:
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