Cat pooping all over the house - help!

In early September my husband and I adopted an 11-month old gray tabby
neutered male from the local shelter. At first he wouldn't eat (he had a
brother at the shelter who was the same way at that time) so I took him to
the vets and learned he had diarrhea so he was on Flagyl for a week.

He was also on antibiotics in case of any intestional problems. A couple
weeks ago I took him in because of a bald spot above his paw. A skin scrape
revealed some bacteria - however, no ringworm turned up in the fungal
culture. He was on antibiotic medication for this for 2 weeks until Friday.
Saturday he pooped right outside of his litterbox which I attributed to
confusion as I had just purchased a pad to put under it. We have stone tile
floors in our house and had a rug under the coffee table until yesterday
when he pooped on it 3 times. I thought at first he didn't like the
different cat litter so I replaced it with Jonny Cat (I used that for our
last 2 cats with no problem).

He again last night pooped on that rug and also pooped in the bathroom my
husband uses as well as the day bed in our back bedroom. He has had
diarrhea which I attribute to the antibiotics and we've never had this
problem with him before. The box is scooped every day and dumped out and
cleaned once a week.

I'm at my wits end and my husband is ready to get rid of the cat (if that
happens we'll take him back to the shelter which is no-kill).

I have a call in to the vet but does anyone have any suggestions?