With the shell back it is important to make sure that the paint is well protected when reassembling the car. There are a few simple procedures that can be followed to make sure that the paint is not damaged and the extra minutes it takes to be careful can be worth a whole lot of time and money in having a repair made.
First you never want to coat the paint with anything that cannot be removed daily. It may be tempting to use some adhesive protection sheets but the paint continues to out-gas for several months and if the paint cannot breath, it will get damaged.
In my case the advantage of being married to a yoga teacher is that there is no shortage of yoga mats around. These are perfect for laying on the paint when working. They are soft, flexible, and just sticky enough to not slide off of the paint. It is important to always inspect the mat for debris before laying it on the paint. We mark 'OUTSIDE' on all the mats to ensure that their orientation is always the same thereby reducing the chance of placing a dirty side on the car.
One place that is super vulnerable are the edge of the wheel arches. They stick out from the body and no matter how careful you are you inevitably rub on them when working in the wheel wells. We protect them using a simple rubber channel we got from the hardware store. It installs really easily and pulls off in a couple of seconds. The thick rubber gives excellent protection from abrasion.