You are way ahead if you can install the trim before painting. However, many of the clips pull so hard there is a chance of damaging the aluminum trim if you install all the clips. I would leave them out till the final install. That said, if they are the expanding style clips, I would still drill the holes and position the clips, in the trim, Just not snap them in. All the bolt and screw on pieces could be installed. Even if it's just the screws on the ends. You will make quick work of the install after paint that way. Any issued can be dealt with easier and the painters will have a line to go to. For hole alignment, I just stuck the tape on one end and pulled it tight and stuck the other side for my line. I did verify it didn't sag in the middle, on the long runs, just to be sure.
This is one of the best trim videos I have found. Most of them seem to be pretty lame or are just selling parts.
https://www.youtube.com/watch?v=5JQYAEa0OGw
Your budget may dictate if you do the trim holes. In my area it's a minimum of $85 and hour and goes up from there. If you are using reproductions will add $ to the install cost. If you pay for the install my hope is they are much faster than I was at it. LOL.
Some of my issues stem from using reproduction body panels. Looks like you have a nice original truck there. That will help you more than you think. As issues always arise from after-market parts. For instance, one tail-light went right in. The other side would not bolt up to the holes in the back of the light. I had to move the holes to make it work.