Found some info on other forums, so I can't post the links here... But the advice given said to:
a) Finish one full round of treatment
b) Do a large water change
c) Do a second full round of treatment
If you're worried about it being too harsh on the fish that have gotten better, could you remove them from the tank, and just treat the ones that aren't doing well?
Or could you try a different combination of meds on the ones who still aren't doing well? Maybe Furan 2 and Kanamycin combined?
ETA: Did some more research on the medications in Maracyn Plus:
* Trimethoprim is used 7-10 days for people.
* Sulphadimidine is used 7 days max for cattle, horses, sheep, pigs, rabbits, cats and dogs... But there's no mention of fish!