@Fanfan26 there are two
separate issues to consider when you are fitting your alternator rotor and stator.
You need to address them separately and not confuse the two.
--1--
Make sure that your stator is running concentrically about the rotor.
So make sure the air gap between the rotor and the stator is the same all the way around.
On pre MK3 bikes this may mean enlarging the three mounting holes in the stator and/or waisting down the diameter of your three mounting studs so that you can wiggle the stator into the correct place.
On a MK3 as per my picture above, you may need to take additional steps using a dremel to remove some material from the outrigger plate.
When you are test fitting, don't forget to have the rotor nut screwed on - this is a sleeve nut, and it helps centralise the rotor on the end of your crankshaft.
Only when you have mounted your alternator, and are happy that the air gap is even, can you think about the second part.
--2--
Are you sure that there is a large enough air gap between the rotor and stator?
I have bought several brand new Lucas alternator rotors and stators in the last few years, and find that the tolerance between rotor and stator is too close for comfort.
I believe there is a degree of crank flex on these engines, probably the most when you throttle back from wide open throttle, and the engine is on the overrun.
So to be safe, on all my new alternator rotors, I have taken a light cut on the lathe.
This allows me to get my 0.25mm plastic shim in, which is the air gap that I personally like to see between the two components.
I have done this procedure several times now, and for me it is peace of mind - something I know I never have to worry about.
Charging seems absolutely fine, and unaffected.