I'm so sorry you lost the brown one. I hope the black one pulls through ok, and it's good that you have a plan to go to the vet if his condition changes.
It's ok to wipe the eyes if they get mucusy, and to cut the hair around the bum if the poop is runny, but the thing is that it's not normal for babies to have mucusy eyes and runny poop. You've got solutions to deal with those issues, but the cause of them isn't going away. With some time, the intestinal issues may clear up. The crusty eyes are strange and I worry about syphilis still regarding them.