Hi Owain,
I can say its not the magneto. The signs your show is a seizure with a few points you had to loock at.
First is the ignition timing, without a strobe you can say nothing about the ignition point. Do you have manual or automatic advance?
If you have a manual timing you can play with. In case of the automatic one ist sometimes realy hard to find the right timing, because itsdepend on wear of camring and and the automatic advance unit. Is the camring worn out there should be a a timing offset. So one pot is running hot.
You on the way with this combination ? Its a hard work for the engine and on the motorway you are full throttle at most time. The fuel consumption is much higher as with a solo, so check your main jet. May be its to weak.
I had the same problem with one of my bikes normal crousing no problem, but at long hills or against wind at top gear, it takes one or two miles and the engine suddenly going harder with a little seizure. This motor had nearly ten soft seizures, an open ear is golden, pull the clutch and the engine stops before the rear wheel blocked. Rolling out and befor standing still release the clutch and the bike run as nothing happend.
Thats my experience.
cheers Klaus