I have to say that if I was a bunny, I'd pick the exact same spots. I think most bunnies would. She also has no concept of pooping or peeing on wire, smell or no smell. She wasvery likelya litter box bunny. (And even if she was a wire bunny, you've got the perfect set up for her to move indoors).

They like to poop at least a little close to where they eat and if they have the choice, poop and pee in a fairly protected area not too far (but not too close) from where they 'live', ergo the end of the hidey box.No wolvesor hawks to grab you when you're otherwise 'occupied'. It'sprobably a little too close to home for comfort, but she was innew surroundings, so she was cautious.
Now that it's ingrained in the wood and in her brain, getting her to stop won't beeasy. You have to eliminate the old option and give her a new one.Shortcuts like just supplying the paper towel won'twork. You'll have to eithertrygradually weening her to the other spot, ortemporarily duplicate her current set-up on the other side and block off the current side. (And concern yourself with the pee, the poopsaren't really an issue).
For the first option, you should be able toget her going in atray or box (or just on paper)byputting it in the spotshe has decided to make her 'outhouse' in her hidey hole. You cancut small cardboard box (as big as you can fit in the 'bathroom' half of the space),or use a low plastic container, and line itwithpaperor even sawdust. Or you can just use cardboard or a pile of newspapers in a pinch. Once she's used to going there,moveit outside the hidey box and block off that end of the hidey box. (And soak the stain with straight vinegar, although with timefor itto air out so you don't choke her with thesmell). If that doesn't work, you may have to block the hidey box off completely until she's well establishedher business in another area, although I'd set up a cardboard box or something for the interim.
I'd move the tray (or whatever you use)onto the wood where her dishes are and just move the dishes over onto the wire. Once she's used to going in thetray outside the hidey box, move it onto the wire, and gradually move it over, or just move the works to the other end of the cage.For the latter, I'd still put it on top ofa piece of wood with the trayfacsimile in the corner. Once she's used to that, putsome soiled litter on the wood in the corner without the box, with the hay orthe hay rack in easy reach.When she's using that corner, replace the wood with cardboard, andthen with paper, and then eliminate it altogether and hope for the best! (at every stage).
Good luck!
sas and the gang