This a complex issue and it sounds as if you have done your research. However, once there have been crystals in the bladder, the urine should be checked regularly. So this is the first step. Have the urine taken out of her bladder by cystocentesis and have a urinalysis and a urine culture and sensitivity performed. If affordable, a bladder ultrasound to check the thickness of her bladder wall and to check for any other abnormalities, should be considered. Some cats will have a normal bladder and urine, but their kidneys are infected or they have kidney stones. This could also cause symptoms. Some stones and crystals cannot be seen on an X-Ray but can be seen on ultrasound. So this does get complex.
This issue is very rarely completely behavioral, and often a physical problem is accompanied by a behavioral component. Once a cat has this problem they are usually prone for life, but once this new episode is resolved there are things that you can do to help prevent new episodes, which I have listed at the bottom of this posting.
You have done all the correct things related to the kitty litter. Now, is it possible that she may have arthritis or pain in her back, or legs? Since she had been let outside there is a possibility of an old traumatic injury that may have healed, but as she gets older the old injury could have resulted in joint instability and secondary arthritis. This can occur at a very young age, as well as in older cats. If a cat has difficulty getting in the correct posture to urinate, or "stands too tall" they may believe that they eliminating into the litter but in reality their behinds are hovering over the edge. There is a different posture for defecating and urinating. The position for defecation may not be painful. An X-Ray to check for spinal, knee, hip, or other joint problems will give you an answer.
If all of the above are negative, i.e., your cat has no joint pain, there are no stones anywhere or infection, than your cat could still have a medical condition known as idiopathic cystitis which is also know as feline urological syndrome, sterile cystitis and goes be many other names. In this disease there is inflammation and swelling in the urinary tract which can cause urination to be painful. The symptoms are much the same as for regular urinary tract infection. However, an anti-inflammatory and anti-anxiety, and anti-spasmodic medication are used along with other therapies for this condition.
For all urinary tract problems the following helps during treatment and as a preventative:
1. Cosequin for cats (or equivalent). This helps the joints and bladder.
2. Cranberry for cats.(there are many chewable brands available over the counter that cats find palatable)
3. All canned, grain free diet. Never give dry food except as a snack!
4. Try to get the cat to increase drinking by getting a cat water fountain (the porcelain kind is best), or by supplying bowls of clam juice and/or broths in addition to fresh water.
5. Have frequent urinalyses performed.
8. Try to eliminate stress for a cat that has stress related idiopathic cystitis
9. Add the Chinese Herbal Formula: Eight Righteous, or the Western herb: cornsilk to the diet.
10. Omega 3 Fatty acids. These are not only for bladder health but help the heart, skin, joints, brain, and other organ symptoms.
11. Additionally, the stressed cat will require anti-anxiety medication, anti-depressants and other medications.
This problem is highly treatable. It just requires consistency and patience.