Did you check the harness wiring diagram you are going to buy? I do not think there is a big difference between the Buell harnesses complexity, so anyway you'll need to open and modify the wiring. But it can be a big difference between the Buell harnesses (different wire color codes, different connection sequence, different wires length etc), so if you are not sure that you can complete the wiring properly and want to keep the original harness to backup just in case you can buy the same harness.
If you have already opened the harness and rotated the engine it should be easy to understand the harness scheme. Just clarify the parts you are going to remove under the airbox, make sure that there is enough space in the airbox to place all parts you want to relocate. Then check the wiring diagram, see each unit you are going to relocate under the airbox and see the wires connected to the unit, each wire in most cases has unique color combination, so it is pretty easy to find the wire and follow the wire route. Each unit has numbered socket, the same numbers you can see on the wiring diagram near each unit, so it should not be an issue to understand who is who. Some wires with different colors in the harness can be spliced together, you can see in the wiring diagram that the wire is spliced with another wires, but diagram does not show the splice location, so if it will be necessary you'll need to find the splice place on the harness. If you are going to splice the wire in another place, pay attention the wiring diagram and carefully check if it will affect the scheme.
Then reroute the wires, keep extra length to trim the wires later. Pack the wires. The wires should be routed far away from heating parts. If it is impossible to route the wires far away from heating parts use high temperature wires and heat sleeves in those areas. If you cannot plan wiring and wires length in advance you can use split heat sleeves, so you can pack the wires in the split heat sleeves at the very end when you have already routed wires and attached units.