1. How long after treating fin rot does it typically take to see new fin growth?
It depends on the fish, its overall health, and the severity of the rot.
As long as the fins aren't deteriorating further, I would consider them "healed." It can take time to see new growth.
I have guy that started to get new growth within days. I have another that needed closer to three months. (He's my high-maintenance fish, and has some health issues.)
2. I am using Maracyn 2 and the instructions say not to use it for more than the 5-day course. Is it safe to use is longer?
I wouldn't continue using it unless there was an active infection. (Ie: the fins were still rotting away.)
Medications are harsh on their systems. Maracyn 2 puts a lot of stress on the kidneys. Using it for long periods of time can start to lead to other, unintended, problems - such as kidney problems.
If he still has deteriorating fins after completing the 5 day treatment of Maracyn 2, I would make a decision:
a) If the Maracyn 2 was helping, but there was still an active infection and I thought it just needed a few more days of treatment, then I might do another cycle.
b) If the Maracyn 2 didn't help at all, I would probably try a different medication.
c) (or I would make some other decision, if the above didn't apply.)
I have read a couple of other places that it should be used until new fin growth is visible (at least a few mm or 1/8" new growth).
Do you have a source or reference for this? I've never heard of it.....
I wouldn't continue using a harsh medication beyond the point where it cured the infection. New fin growth can take quite awhile to show up, especially in a fish that's been stressed (by a new tank, an illness, etc).
IMO, treat for one cycle (5 days). Then reassess the situation.
If his fins aren't getting worse, then I would stop the antibiotic and just monitor him. As long as no additional rot appears, I would just wait and keep watching for new growth.
But, personally, I wouldn't use more medications unless I saw signs of an active infection or further rot.