So glad you asked this question. Going to be doing this soon myself.
Hubby is almost done with building a much larger coop. We're going to put the old coop at the other end, but first are going to clean it out well. Hubby did not waterproof the nest box on the old coop and used that type of wood that absorbs water easy (why I have no clue), so it started rotting and is falling apart. It's not a very big coop, so just gonna take the nest box off and close that area up - with water proofed wood this time. In it's place I'm gonna have him build something I can put a few milk crates in (used milk crates in it before and they prefer the crates to the little kitty litter boxes, which had plenty of room for them)...since the coop isn't that wide, should be able to reach eggs easy. Gonna have him drill more holes for ventilation and build shutters for the windows (tried wrapping in plastic last yr. and it didn't do a great job...so want shutters this year to keep the cold out. The old coop is getting a new bottom put on it as well.
Gonna get some dirt from my parent's house (they have some left over from having a pool put it) and level out any sunken spots in the run. Then gonna put construction sand over that.
Dividing the run with chicken wire and a huge dog exercise pen I have so I'll have a door to get from one side, as I only have one coop door. I have bantams, so I have to make sure the run is divided well, as they can fly.
Have had the new birds in quarantine for months. Reason being is that my birds got Coccidiosis from the place I got them from. That's the only thing I can figure, as they're in different crates and bins that I'm using as brooders in a spare room no one is using at the time. Thankfully only lost one very young chick. Treated everyone and used probiotics to get their health up. It's been months since that incident and everyone is doing fine now. Gonna worm, bathe (the new flock, as they need it) everyone and dust them all down for parasites (they don't have any that I can tell, but just to be on the safe side).
Have to start integrating birds that were quarantined in the house, which I plan on doing a little bit at a time, like in the bathroom with me in there to watch for any squabbles. Gonna do the more laid back birds first, then the others, until everyone is integrated.
By that time hubby should be done with the coop, the run should be all set with sunken areas filled and sand put down, old coop should be ready to go and run should be divided.
Then put new birds outside on their side and slowly introduce them to the existing flock.
Hope all goes well for both you and I Hunterhart.