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Hello, I'm Dr Gary. I've been practicing veterinary medicine since 2007. I look forward to helping with your questions/ concerns.
It sounds like you may be dealing with another UTI or even pyelonephritis (infection of the kidney). Less likely, there could be stones in the bladder causing the irritation and urinating out of the box. The defecating out of the box is probably due to painful urination and then litter box aversion.
The dark urine around the vulva (urine hole) is likely a mix of bacteria, inflammatory cells, protein and blood. It should clear up once the UTI is under control.
The next step would be getting a urine culture directly from the bladder to see what bug we're dealing with (usually e coli) and then to determine which antibiotics will work against it. I would also check her kidney values to make sure they didn't take a hit with the infection.
I hope this helps, let me know if you have any other questions.
You're welcome, happy to help.