[Jonboy]

Getting the fenders to line back up isn't too bad at all. If you are leaving the radiator support in place, they will bolt up to the same place in the front. Take note of where the shims are in the rear, and mark your hood hinges. The hood hinges mount to the cab, so that shouldn't change by taking the hood off.

On the frame, you can just spray the undercoat, it doesn't need paint under it. The bed braces are important if you plan to carry anything heavy, as they distribute the load and keep the bed floor from sinking. A word of caution, if you are going to pull the bed and/or cab, make sure you have the replacement bolts first, especially if this is a daily driver.