Do all of your mods first. Drivetrain, suspension, sheet metal repair. Then take it apart...that way you know what you will need and how it will fit beforehand and you have less risk of damaging the new stuff (paint and body) later on trying to make all the mods fit together. Definitely make an investment in 2 and 1 gallon zip locks as well as quart and sandwich size bags. DOnt forget the sharpies. Label everything, use tape as well if you need to. You will be surprised what you may need to recover later on. After disassembly, finish any sheetmetal work, frame clean-up/repair--but do all the additions of the new stuff beforehand. Blast, paint, powdercoat, reassemble, lube and drive. There will ALWAYS be modifications after the fact...but try to minimize them by getting a good plan of what you want the Bronco to do, ride like and how you plan to use it.
Its not a cheap proposition, to undertake a frame off, but its a very cool process. Take your time. By doing alot of the mods ahead of time, you can drive it and make changes to your plan before you ever begin to tear it down...you can also defer the cost of many of your projects over time. Since your going to be spending alot of money, make sure--as much and you can--that what you'll end up with is what you really want. thats whats really important. Mods first, then tear down, build up.