Sadly they were gone when I got home
You talked about several different groups/ages... When you say they were gone, are you referring to ALL of them? or the 5 months olds (no longer babies, sorry)? The newer 8 week old chicks? I'm sorry but also not clear what happened to cause "gone"... did they escape and wander off? were they taken by predation? Did the older birds do the velociraptor thing and eat them? OK, aside from all that, here are a couple of observations/answers:
1. Chicken wire is useless as protection from predation. It is designed to restrain chickens (or rabbits) from leaving their designated area, or keep them from getting in to an area they are excluded from (garden). Snakes/weasels/mice can go right through the holes and any sizable predator can rip right through it in minutes and be off with a chicken dinner. You really need something stronger like hardware cloth (1/2" is better than 1/4" as the wire is heavier gauge). You cold also alternately use 2"x4" welded wire fencing or even scrap chain link fencing to "back" the chicken wire. It won't stop small predators but will keep chicks inside the run and large predators out. Save the existing chicken wire to use to cover the run to keep birds of prey out.
2. That back door needs reinforcement and a much better/stronger/more secure latching mechanism. The way it's warped out at the bottom and in at the top provides a gap that chicks can escape and a place for predators to gain access leverage. Raccoons especially are very adept at popping those latches like what you have and walking/climbing right in for dinner.
3. The entrance holes into the nest boxes look kinda small to me, but if your birds fit through and are using them, then there's your answer... they're fine. It's a chicken coop, not a 5 star resort hotel. The chickens only care about function.
4. There are some on here who disagree, but IME chickens don't "perch"... they prefer (In order) A) the highest point they can reach to roost and B) prefer to stand more or less flat footed with their toes curled over the forward edge of the roost. They then hunker down on their keel bone (for balance/support), & in cold weather it allows their feathers to keep their feet/toes warm. Yes they WILL "perch" on the thin edge of a sheet of 1/2" plywood/particle board or a 1" pole, but generally it's because that "perch" is higher than their provided roost. High & wide is better IMHO... at least 3.5" for large fowl.
5. All of this comment is based on large fowl birds: Not sure of the size/floor area of the coop, but please keep in mind that adult chickens really need ~4 square feet per bird inside. Each chicken needs ~18" of linear space on the roost in warm weather but can get away with ~12" in really cold weather (they'll snuggle together for shared warmth). If multiple roosts, they should be at the same height and at least 24" apart horizontally to prevent fighting, feather picking, and pooping on the lower level roosting birds.
6. The run door needs a latch down lower as a raccoon or skunk can pull/push the door open enough to gain access with the latch so high up.
7. Yes, you can make the run large enough to encompass the swing set. You can make it whatever size you desire. Large fowl really need ~10 square feet per bird inside a run. They can get away with less if they are allowed to free range. Just keep in mind that if your birds climb up onto/in the swing set, they could potentially fly out.
Good luck moving forward!