A real pain .. could be anything.
Feel free to use a house mains 13A fuse whilst you trouble shoot, easier / cheaper to source.
I'd suggest bouncing / wiggling the loom / turning the headstock everything in an effort to promote blowing a fuse - ensuring that the circuits are all live, eg indicators, lights on etc. If this is 'successful' you've at least narrowest to a problem area.
Wrt the suspected ignition circuit, you could try 'hot wiring' it direct from the battery +, ie take a length of (at least) 5A wire (with an in-line fuse if poss) and connect it between the battery and thence as 'upstream' of the coils as you can get, ie within the headlight(? PPR) directly to the black input to the IGN kill switch, or failing this the black / white that comes from it. (if the latter beware the IGN will be on 24/7 and so you may damage coils if left powered too long - the in-line fuse would help here ie used as a switch. Furthermore, in a spill the kill switch would not work)
Moving on... the ignition circuit would now be completely isolated from the rest of the bike circuitry, and one way or another could be ruled out.
Simon