Why do you want to take it off in the first place? That sounds like more work than necessary. What alignment are you referring to? If it’s still on the truck, it likely is aligned. I would leave it in place unless you have a major need to remove it. I installed my wood with the bed on the frame after paint. It went very well. Work from the outside toward the middle. If it’s very nice and shiny wood with shiny strips, wear your comfy socks to keep it shiny.
