The Gen 2 flywheel has two triggers.
Staggered, with a single pick up in the cover.
The Gen 1 has a single trigger but with two pick ups in the cover.
You have a Gen 1 cover, two pick ups.
But you bought a Gen 2 pick up assembly.
The Gen 2 flywheel must have the one trigger ground off to work with the Gen 1 pick ups.
Is there a reason you can't use the Gen 1 pick ups?
Were they damaged?
Otherwise, you'll have to do some swapping around to make stuff work.
If you are trying to use the new single pick up, then the flywheel will not have to be modded.
But you will have to mod the wiring (and possibly change the cover) to work with the Gen 2 pick up.
I can't remember if the cover will have to be changed or not, @Saabnut
could 100% answer that.
Unless there is some specfic reason you can't use the existing Gen 1 two pick up system, leave it be and mod the flywheel.