We got two shelter cats, knowing that one had very uncertain health record. After around 18mths, she developed cancer and we had to have her put down - first time I really saw my dh cry, the vets had a special side door so you didn't have to walk through waiting room in floods of tears.
I know it's a hard decision to put a cat down, but it's the right one if he's in pain. For us, we just reminded ourselves what Jess had had, that she wouldn't have had if we hadn't 'rescued' her. Exactly the same for you, wherever you got your cats from. Best wishes.