I did a little reading about struvite crystals, and it appears that they are not unusual with a UTI. I know your vet said that he didn't have a urinary tract infection, but I read that they don't always show up on tests. This article that I linked below might be helpful to read. I hope you find out what is causing his crystals, and I hope Deuce gets better soon.
Canine Kidney Stone and Bladder Stone Prevention - Whole Dog Journal Article
"The importance of testing
It’s important to know that urinalysis can’t always detect a bladder infection; urinalysis may appear normal as frequently as 20 percent of the time when a urinary tract infection is present. For this reason, if your dog shows possible signs of infection, you need to request a “urinary culture and sensitivity test.”This will verify the diagnosis (in some cases the problem is something other than an infection) and, if it is an infection, it will reveal which antibiotic will be most effective for treatment."