it's always great to have clean pods.

as time goes on and i have more and more beans of the bulk kind i've gotten more generous with the worms and let them have the pods that look the worst instead of me going in there and getting that one bean from that pod where all the rest of the pod is rotten from dragging in the dirt too long or getting rained on too much. i do make an exception even still for certain rows of beans where i know i've planted a lot of odd seeds because i do want to see each and every seed i possibly can from that row...
There were maybe a half dozen moldy pods in 60' (well, 55' after the bull incident) of trellis, which I just tossed over my shoulder into a different row. In every case it was a pod that was sitting under decomposing leaves that have fallen off. Red Turtle, growing a few hundred feet away, lost maybe 10% of its pods to mold. I think the lower leaves falling off from Seneca Allegheny early is key to saving those pods but that's a guess.
@jbosmith when i have a lot of pods that i've picked and some of them are dry enough and others aren't quite ready i sort them out and leave them to dry in the sun for a day.
this serves two purposes, one is to let the bugs that might be in there to crawl away and the other is to give the pods one last blast of sunshine before they get put into large paper bags. the paper bags will let them breath out any remaining moisture without rotting and they can be stored that ways for however long it takes for you to get around with shelling them out.
the not quite dried pods i'll either leave in flats/aka box tops until they dry enough to shell out or i might even shell them at that stage to make more room for what i'm in the middle of harvesting next. the beans themselves from the shelly stage take up much less room and i rotate them once a day so they won't start rotting, but again i don't put them into plastic containers, i use cardboard flats that will let some moisture wick away and breathe better than plastic.
Luckily, my zone 3 gardens have never had any bugs that I cared about! (knocks on lots of wood) When I harvest from my community garden, which has all the bugs, the beans get shelled, their pods dumped back into that same garden, and the beans go into the freezer, all pretty quickly so as to minimize the risk of introduction to my house where other beans are drying.
Otherwise, your method is pretty similar to what I do. I also collect a lot of pods in empty beer flats, especially of the varieties where I don't have a ton, and sometimes put them in the sun early on. I usually just leave in front of the AC's fan to keep the air moving around them unless they're extra wet or have been frosted, which makes the wet pods turn to mush pretty quick.
I got home late last night and everything stayed in the same paper leaf bag until this morning, so they were all in the 'not quite dry' stage, the dry pods having absorbed moisture from the not-so-dry neighbors. None of them are super wet though. This whole batch should be dry in a few days. The paper towels are also under there for the wicking you mention. In the past I've used wire shelves for added airflow, but these are bigger, were easier to move, and should be good enough.
Sometimes, when an early frost threatens or I otherwise have bushels of pods to deal with, I'll also stack field crates on top of each other with a few inches of pods in each and paper towels at the lower levels to keep beans from falling all the way to the floor. That doesn't work quite as well but I only have so much space for shelves.
by the time the middle of winter comes around pretty much everything is dried well enough to then go into more closed up containers and i won't open many of them until it is time to eat them or whatever else i might be doing with them.
Same, though once it gets cold and/or dry, I also start canning a bunch whenever I have a free evening. I eat 1/2 to 1 cup of beans a day with my partner eating them on occasion, so it takes a lot of jars to get us through the year. It's nice to know where they all came from though!