From what I can see, I wouldn't be too concerned... they're not that bad. I'd be more concerned if they were bloody, black (apart from natural colouring) or missing finnage very close to their bodies.
I would bet that he is either biting/chewing his fins... or he's catching them on something. I don't think this is from excessive flaring as the splits would likely be much further up in his fins.
This could also be mild fin rot, b/c you are battling the ammonia in your tap water, and battling their water params constantly. I think all you can do is continue with what you're doing... and hope that when your tanks are finally cycled... they'll heal up nicely and you won't have to worry anymore.
Do keep us updated, either with pics or reports, on how they're doing.
Mr. Bubbles is gorgeous! LOVE, love, love his colouring!!
Michele
