Princess was spayed when she was only 6 months old & she had a UTI not long after. Vet mentioned the anatomical defect & said we can do the dye if it occurs again. She has not had another UTI...but recently (she's 5 years old now), she had struvite crystals in her urine, but no bacteria or any sign of stones.
The struvite crystals will form into stones if the pH is consistently on a higher alkaline level & it's almost always associated w/an infection. A healthy dog's pH is slightly acidic, @ 6-6.5. Struvites form @ higher alkaline pH @ 7.5-8 (this is where a human's should be).
Since your little one has stones & a UTI, it needs to be cultured & an antibiotic sensitivity done to see which antibiotic will be most effective. It needs to be sent out to a lab & it costs around $150-200, depending where you are. Has an x-ray been done? Struvite stones can be easily seen on an x-ray. Is she on a prescription diet to help dissolve the stones? Some say a special diet is not needed since struvites can be dissolved. So what you're doing is good, 'Liquefying the diet' is key (learned this from Cathy too).
Be very careful w/supplementing anything acidic like cranberry (long term) as it can cause oxalate stones which require surgery for removal.
All About Oxalate Bladder And Kidney Stones In Your Dog And How To Manage Them