Stinky Rats

Is it a pee smell? or a Poop smell? What are you feeding them?
Is the smell worst on his underside? If its a pee smell and he's the only one and you clean the cage every day than there is a chance he has a urinary problem and needs treatment. If he's an older Rat or a Fatty he might have a penis plug. Is his underside wet with Stinky Pee?
Try and narrow it down and you'll know what to do next.
Spider

Are you using Carefresh in the litter tray? if you use something uncomfortable they won't want to lay in it.
I use Aspen in my tray, its hard and lumpy and they don't lay in it anymore. I used to confetti shred unprinted newspaper but it became they're second bedroom.
Spider
A little tip: most wood litters have some dust no matter what they say, I go outside with a big plastic collinder for spagetti and grab a big handful of litter and toss it up and down for a minute or 2. Its amazing dust and small crap flying everywhere, the result is zero dust, and it only takes a sec to fill the tray.