If this belongs better in behavior, please switch.

Beaumont, my 5 y/o mini-rex went to the vet a week and a half ago. He wasn't eating or drinking or pooping and had been looking very uncomfortable. They said he had a respiratory infection and tummy blockage and was in a lot of pain. They gave him some medicine and fluids and he was actually a lot better that night- eating and drinking. However, because he was still in pain he was moving very little in his condo. He was peeing and pooping wherever he happened to be sitting, when he moved I cleaned it up but he seemed to be too bothered to make it to his litter box. 

He has since improved a lot. He's still not laying down much or spending much time out of his condo, but some. I've been giving him Metoclopramide syrup 3 times a day and baytril liquid once a day. His poops look normal now, he's eating/drinking and pooping regular amounts. He spends most of the day in a corner of the condo that is impossible for me to get to, he hates the medicine and try's his hardest to stay away from me (my husband has elected to be the good guy and not give any medicine) . He is sitting normal and doesn't look tense but I'm not sure if he still doesn't feel well or is just trying to avoid me. Either way, he is still pooping and peeing pretty much wherever he wants. Occasionally he will use his litter box but opts to poop around it and pee around it or where he's sitting. 

I'm trying to clean everything up asap (and he isn't pooping/peeing anywhere outside of his condo when he happens to be out) but it really upsets him when I'm in the condo right now and I feel like it's not helping. But I don't want his litter habits to wain.

Has anyone had a similar experience?
Could this be caused by the medicine?
Does he not feel good?
Should I keep cleaning everything up immediately?
will he stop this on his own?

Help!

What diet is your bunny on?  Diet is the primary cause of digestive problems that you are describing, so that is where most of your effort should go right now (lots of grass hay and leafy greens- avoid pellets, at least for now, and anything else you might be feeding your rabbit).  I'm glad you bunny is improving, but 'bad toilet habits' are very common when rabbits don't feel good.

I would think it still due to his having been ill also.

Something to try is use a box with a low side to access it. If unwell, the effort of getting into the box might be a deterrant for him. Just a new box alone might make him curious enough to go there. Also consider the litter you are using. Is it something that would further irritate his respiratory system at the moment?

Beautiful rabbits!