That's great! I'm glad it's all turned out and he's doing well for the most part. Him peeing outside the litter box could have a health cause. He's been on antibiotics for a while, so maybe he's developed a yeast infection. If this unusual behavior continues, maybe have the vet do a urinalysis to see if there might be a problem there.
If you're keeping the hay in a plastic container that's covered most of the time with a plastic lid, and if you're in a humid environment, this can cause hay to go bad with mold. That could explain him not eating his hay well. If you think this could have happened with his hay,
do not continue to feed it, but get some new hay and see if that makes a difference. Moldy hay can make rabbits very sick and will have white or black spots, white dust, and/or have a sour or musty smell to it. In a humid environment, hay especially needs openness and room for airflow to prevent mold growth.
If it for sure isn't moldy, maybe buy and new bag of hay, even a different variety of grass hay, and see if that makes any difference. If not, maybe he's developed a dental issue. If you take him in for a urinalysis, it would be good for the vet to check his mouth as well.
https://furrybutts.wordpress.com/2008/06/25/how-to-store-hay/
I always put a blanket down and lay down on floor with him and he’s peeing close to where I lay same spot or on the same rug in the same corner. But he’s not done that since I had him so will do urinalysis to just ease my mind as long as vet is able thank you for your help with him 
