You can open up the cover and remove a lot of the wires and make the harness much more simple.
As far as the white wires you need all three to have the alternator work.
You might want to look through the "Some wiring diagrams" thread . You can find links to it up in the XS650 Tech section.
Find one that has the items you are using and use the wires and connectors from your harness to build a new harness. I have had some harnesses that have very stiff wires, others the wires are much more flexible. If yours has stiff wires I would suggest you use new wire to replace the old stiff wire. Use wire that matches the stock colors, this will make trouble shooting easier.
The stock harness has all the right plugs and connectors so all the stock parts you want to use just plug in.
Leo
As far as the white wires you need all three to have the alternator work.
You might want to look through the "Some wiring diagrams" thread . You can find links to it up in the XS650 Tech section.
Find one that has the items you are using and use the wires and connectors from your harness to build a new harness. I have had some harnesses that have very stiff wires, others the wires are much more flexible. If yours has stiff wires I would suggest you use new wire to replace the old stiff wire. Use wire that matches the stock colors, this will make trouble shooting easier.
The stock harness has all the right plugs and connectors so all the stock parts you want to use just plug in.
Leo