Glad to hear the feliway may be working
I really hate to be the pessimistic one, but with my experience, once a cat has got it in their head that they "hate" a cat, it's very hard to get them to be friends, especially if one is very timid and the other is aggressive. I'm not saying impossible, but it really depends on the cats (really I mean Bubbles).
Puddles and Sweet Pea got along when they were first introduced and then Puddles made the mistake of hissing at one of Sweet Pea's kittens while Sweet Pea was there and Sweet Pea attacked Puddles and that was 4 years ago and Sweet Pea is still always trying to attack Puddles. We now keep them separated all the time and we tried everything, even drugs like you have, to calm Sweet Pea down. We don't even try to get them used to each other anymore, it's just seems to be better for both of them to be kept separated.
But if you find a way, please let me know, I would love to hear it!