One of the toughest parts of this job will be the disassembly and reassembly taking care nor to dirty the white and orange basecoat. Your idea of spraying the clear is good but I would use an intercoat clear instead of a topcoat urethane clear. Light colored basecoats attract fingerprints and staining very easily, if you apply two coats of intercoat clear over these colors before disassembly it will protect the light colors and provide a surface you can actually clean. Another plus to the intercoat clear is it is thin like BC.
Your idea of using a topcoat clear will also work but it also opens the door to possible lifting problems when you apply the third color, fresh urethane can be really sensative to solvents.
Intercoat clear can also be used to freshen the basecoat prior to clear application if you're worried the BC has dried to long. Get all your color work done then apply a coat of intercoat clear, let it flash good then apply your urethane clear.
Good luck with the project, you've got some stress ahead of you pulling that freshly colored sheetmetal off and then reinstalling it. Do a few test sprays to get your fade technique ironed out. Take your time, Bob