That's a good diet.
I include that into my food mix. Prior to Zupreem, I only used 8-1 Ultimate and Drs. Foster and Smith Ferret diet. After I added Zupreem, I have to admit, it did make my ferret's poop smell more than usual.
But their poop dries fast, so the smell usually doesn't linger. I think the main problem is that you're putting it in a sealed container so the poop just sits and stays wet. I can only imagine that the odor from that container is like hitting a wall.
Flush the spot cleanings or dump it in a plastic bag and put it in the trash can.
As for nail clipping. If you can't use ferretone, you can scruff her. Scruffing doesn't hurt the ferret. Ferrets are in fact calmed by it. She will go limp when scruffed. (Scruffing is also good to use when syringing liquid food)