This is very likely due to upper respiratory viral infection picked up before you got them.

You can read about these here

http://marvistavet.com/html/feline_upper_respiratory.html

Viral infections are not cleared up by antibiotics but secondary bacterial infections can be cleared with them.

How kittens react to the viruses depends on their own immune systems so each could react differently.

This site has some good pictures on giving eye meds to cats

http://www.vetmed.wsu.edu/ClientED/cat_eyes.aspx

A really uncooperative kitten can be confined in a big bath towel so you don't have to try to handle feet when trying to do this if you need to do it by yourself.

Hope this helps you!

If the tear duct in the eye corner has popped out and its not just the third eyelid that is inflamed then surgical repair of 'cherry eye' is the best choice.

http://marvistavet.com/html/cherry_eye.html has some info on the reasons for surgical repair though it talks mostly about dogs it has a picture of the eye issue.

And here is more on cherry eye in cats (just close the pop up to read the info)

http://www.petplace.com/cats/cherry-eye-in-cats/page1.aspx

I suspect with Angel you were dealing with a better developed immune system which was able to fight off the virus.

You said he went through a lot of stress and stress can make infections worse, but as he came through the trauma and is still a nice kitten that tells you he handles stress better than many cats which might contribute to his ability to fight off infection.

You didn't mention if the kittens were tested for viral infections such as feline leukemia as harboring that sort of infection can lead to trouble with clearing other infections.

http://www.peteducation.com/article.cfm?c=1+1316&aid=213 has info on FIV

and this site on feline leukemia

http://www.vet.cornell.edu/fhc/brochures/felv.html

And also if they are not totally clear if internal parasites that can impact recovery time as the parasites 'steal' nutritoin from the kitten. They sometimes need 2-3 wormings to totally clear an infection.