Firstly, just because you were told they were indoor cats, do not presume it is the case. I was called once about a female cat that was an indoor only sole puss and she then gave birth to a litter of kittens!
I would get the boy tested for felv/fiv just for your own peace of mind. Do you know how exactly he lost his eye. Could have been a spat with the other cat in the house and that one was most likely unvaccinated as well,so better to be safe than sorry.
I would also keep him separate until after the second jab. The first vaccination can sometimes bring on flu like symptoms as a side effect so I always keep them separate until a couple of weeks after the second jab, to be on the safe side. Also, if he has access to the cat flap once he is released into the house, I would keep him from getting out until he has been neutered. Being four months now, he is only a couple of months away from that anyway and he can be microchipped at the same time. The last thing you want to do is go through all the introductions with the other cats for him to to go off looking for luuvv.
How close are the two of them? Bear in mind that as the girl is deaf, she may rely heavily on her "brother" and it may be very stressful for both of them to be split up.