Firstly, welcome to the forums!
Let’s see if we can help.
For starters, you can read this helpful page to learn more about litter training. The key is to make the bunny feel as secure as possible in the territory that will be hers, so that you can avoid territorial marking. A good way to do this is to start with a small space, then slowly allow her to expand her world. It will still take quite some time for this to fully sink in, however – even months! Similarly, are you positive that she is a female rabbit? If so, you will definitely want to get her spayed as soon as possible, if she isn’t already. This will not only help tremendously with litter training and other behavioral issues, but it will greatly reduce her chance of developing reproductive cancers.
Now onto the cages / enclosures. Good for you for putting something down on the wire floors, because yes, it is bad for their feet and can cause a condition known as “sore hocks”, which is a nasty, painful business. You don’t have to worry so much about this right away, unless she’s been living in there for a long time. Take a look at her hocks (back feet) to check for blisters and sores.The minimum recommended size for a rabbit is 12 sq. ft. (4 ft. x 4 ft., etc), so that x-pen you have now would be perfect to function as her actual living space. If you get a second pen, you can attach that to her “house” pen to give her a huge space to run around in, or you can consider free roaming her in a single, bunny-proofed room of the house. Perhaps later, you can even consider making her a completely free roaming rabbit. Another option would be to build her an NIC condo or get her an extra large dog crate if you’re low on space. The dog crate is only really recommended, though, if she’s out basically all day long and only goes there to sleep.
For the fleas – is she living indoors? If not, we highly recommend you bring her indoors. Rabbits that live indoors tend to have longer, happier lives and this will basically eliminate the chance of her getting fleas, mites, or other parasites, though it does still happen, especially if any other animals are around. There are a multitude of ways to treat these parasites. Consult your rabbit-savvy vet (and if you haven’t found one yet, check this page out to find one near you).
Good luck and welcome again! 