What did the stool sample show? Was he treated for any intestinal parasites? Some of them don't always show on tests so a vet might suggest a treatment anyway to rule them out. Metronidazole was prescribed for my cats when they got extreme diarrhoea of unknown origin. You can use Immodium on cats but you would need a vet to okay that and give you the dosage. It's good only short term.

Is it possible he got into something in the garage where he lived that did damage to his intestines?

I adopted a cat several months ago from an animal control. The cat had been on the streets for months and was overgrooming from the stress of being in a small cage for months. At first I thought he had allergies and put him on a very restricted diet but I've found over time that stress is the major factor both of his terrible, and sometimes bloody diarrhoea and his overgrooming. Now that he's settled into my home, he can eat anything.

Your cat might have several issues going on at the same time which makes treatment difficult.

Can you confine him to one bedroom and throw a sheet of vinyl flooring over the carpet?