I have two feral cats and when young I kept them in a small to medium dog cage w/litter box,food and water. They already knew to use the litter box for both "jobs" and has never been a problem with any kitty I have had. I kept them in the cage so they wouldn't hide and I couldn't find them and they wouldn't be able to get use to us humans. This would solve your peeing problems and the 1st thing I would do if I had this problem and then take to a Vet. to make sure there were no medical cause.
We work all day, but, in the evenings I would take them in a room with no hiding place and sit and hold them and pet them, I did this until they got use to me and would come to me, gradually letting them loose in the room and then in the rest of house. 1 is now 14 yr.s old - other is 10 Yr.s old. They are both wild about me, still kind of scared of strangers but, not Hubby and me.
Urine in unaltered kittens have a very strong odor.
I hope you find a solution to your problems, hope this helps.