Question... is there a reason you haven't had her fixed? It is better for her health (lower incidence of cancers in spayed cats) and it does tend to lower the incidence of litter box issues. I have read many times that intact females will often urinate all over the house.
Here's something else... can you put her in a cage long enough to let the area be cleaned and dried and then make it so that she cannot get back there anymore? When we had litter box problems with Whiskerville cats or fosters, sometimes being in a large cage (big enough for a litter box plus, food water, and a place to curl up) for a couple days was enough to reinforce that waste only goes in the box, since her living space would be so small and she'd get that she doesn't want to "go" anywhere else but the box. If you got her fixed, that would be a good time to try it. If you don't have a cage, a local rescue might let you borrow one. You can get her fixed, bring her home, put her in the cage while she recovers and your floor dries out, and then after a couple days, let her out and see what she does.
This is similar to the ones we use, but we tie a milk crate to the top and put a small fleece bed in it, which acts as a loft over the litter box and gives a nice place to nap.
http://www.petco.com/product/13372/PETCO-Premium-2-Door-Dog-Crates.aspx?CoreCat=OnSiteSearchAlso, sometimes a recovery (from illness or surgery) can give you a chance to bond. Granted it didn't work with Fabi and me, but it did work for Chance. ESPECIALLY when they are still very groggy from pain meds. Cuddle, cuddle, cuddle while she is high and see if she forgets in the fog to put up resistance.