Out of ideas for litter training--please help!

I am having a lot of difficulty training my former stray cat to use the litterbox. When she was confined to one room she did fine after about a week or two, but since she's had the run of the house, she has regressed considerably. I have a litterbox upstairs and, as of yesterday, two litterboxes downstairs (one in the bathroom where I've always kept it and the other on her favorite non-litterbox potty spot).

Any suggestions would be much appreciated. I am seriously out of ideas.

What I have tried:

-Cat Attract in the litter. I think this helped initially but it doesn't appear to be doing anything now.

-Enzymatic cleaner, felaway, and No Spray. All of htese keep her from returning to hte same spot, but then she just finds a new non-litterbox spot.

-Putting a litterbox where she likes to poop: She's found a new "bathroom"

-Closing cat in a small room with the litterbox. I tried the bathroom, but she's figured out how to open the door. When she was in quarantine she was confined to my study, and I am tempted to try that again but I would consider it a last resort as it made my other cat very anxious.

-Placing her in the litterbox after she eats or after she goes somewhere else and providing positive reinforcement around the litterbox. So far, not much luck, but I'm working from home for the next couple of months so I'm hoping increased supervision will make it go better.

What worked at first:

She spent her first month with me quarantined in one room and, by the end of that she was using hte litterbox 90% of the time. That litterbox is still set up in my study and I use the same litter.

-Cat Attract

-Putting litterbox where she likes to go then slowly moving it to a more desirable spot

-Dirt and leaves over the litter (this was only necessary for the first two weeks or so--by the end she was using normal litter)

-positive reinforcement around the litterbox

Is she spayed? Has she been checked by the vet recently?

We've spent a fair amount of time at the vet, as she was in pretty rough shape when I rescued her--chronic dental infection, anemia, and severely underweight. However, the vet does not think there is a medical cause for her litterbox avoidance--kidney function, TSH, blood glucose, etc are all within normal limits. The only thing that could be contributing is that she's on high-dose steroids and one of the side effects is having to pee a lot. But that doesn't explain the pooping outside the box.
We're pretty sure she isn't spayed--the vet is sending off an estrogen level to double check so we don't subject her to open abdominal surgery for nothing.
From a medical standpoint, she has improved considerably and this week she was cleared for surgery to definitively treat the dental infection (we've been controlling it with antibiotics and keeping the inflammation down with pred). We're going to schedule the procedure once the estrogen levels are back so she only needs to be anesthetized once. After surgery the plan is to discontinue the antibiotics and taper the steroid.

You've already tried a lot of things!  Cat Attract was what worked for my old boy who kept going outside the box.  

There's a whole section here on TCS about litterboxes:  http://www.thecatsite.com/atype/45/Cat_Care  You'll see several articles on litterbox maintenance, placement, etc.  Perhaps you'll see something in one of those articles you haven't tried yet?  

My thoughts are

1.) She has developed a UTI. This wouldn't be diagnosed by bloodwork. A urinalysis would need to be done

2.) She isn't spayed and thus a behavioral problem that will likely be corrected after the hormones get out of her system. (It's a common misconception that females do not "spray"/mark their territory.) This sounds like the more likely cause.

I definitely think some of the accidents are spraying and I am hoping we will have a clearer picture once she is spayed (though I have known enough neutered/spayed cats that spray). Is it worth trying aggressively to litter train her now or should I hold off until she's spayed?

UTI is very low on my list given that she has completed two courses of fluoroquinilone antibiotics, which should provide good UTI bug coverage, on top of the clavamox she remains on until surgery.

Have you tried using Cat Attract only in the litter box? They also have a new Attract litter said to offer a "taste of the outdoors" perhaps that might be worth trying as well?
You could also try putting dirt or sand in another box as well.

Does she use the litter box at all?

If she is marking her territory, I would think that she will continue this behavior until she is spayed. I know it takes a good 60 days for testosterone to completely get out of an adult male's system, I suspect a female may be the same?

If she continued to mark after that, perhaps harness/leash train her so that she can mark the area OUTSIDE the home, rather than in?