Oh they are gorgeous! Are they rescues? They are big boys of they are young ones!
I'm on my phone so I may miss something but re washing the chew tunnel, it depends on what type. I wipe down everything, including cardboard, and you can soak the plastic ones. We have hundreds of hammocks and bits of fabric that get used as hammocks. You may find that if you put a few up they may start using them more, or they may not have used them as it's hot or it may just be that they don't like hammocks, our lone boy refuses to climb and loves his box, I can count on one hand the times I've seen him in a hammock without me having put him on it.
Definitely try different substrates, I can't remember what we used as we switched to fleece for all three cages in the end. Our boys were allergic to everything though so we didn't really have a choice.
Was the two storey cage advertised as for rats? Usually P@H stock the Jenny as their token rat cage so it should be fine in terms of the size not contributing to the smell. She may need to do smaller cleans in between to keep smell down, so use a scoop to get damp substrate out every night, wipe down any shelves and remove any particularly smelly toys. We spend no more than ten minutes doing all three of our cages every night, but we don't have any shelves, only hammocks.
How old are the rats and how long have you had them? If the smell is a recent thing then it could be hormones triggering them to mark more, always fun -_- our girls mark more than the boys do, they also pee down the bars the dirty sods. The boys have never done that.