What's wrong with the stock dual tower coils? The best fuse system is a simple panel. My personal favorite is the Eastern Beaver PC8. Centech make some that are adequate and there are others.
If you must rewire it, I suggest you place the wiring in place on the bike and connect up as much as possible and peel open the harness. With the wiring diagram in hand, you can then surgically remove anything that you don't need and then seal it back up leaving the ignition wiring and connectors intact.
That way you will also be able to see the way that components like the pulsars, coils and CDI are connected in case you want to move something and have to lengthen any wires.
Do you have nay pictures of the bike as you bought it and where it now is that we can see?
If you must rewire it, I suggest you place the wiring in place on the bike and connect up as much as possible and peel open the harness. With the wiring diagram in hand, you can then surgically remove anything that you don't need and then seal it back up leaving the ignition wiring and connectors intact.
That way you will also be able to see the way that components like the pulsars, coils and CDI are connected in case you want to move something and have to lengthen any wires.
Do you have nay pictures of the bike as you bought it and where it now is that we can see?