Hi Otterfun, Anhel asked me to take a look at your thread. Thank you for all the information you've provided. It makes it easy to help you. :)
From what you've been reporting, Fred's fins are in the process of healing. Based on your info, it doesn't sound like he had a very aggressive rot so I don't think you need to do any advanced treatment. Stress Coat and a healthy diet should do the rest.
Your pH could possibly have spiked a little because of the limestone gravel (if you are sure it is limestone) or as a result of higher levels of dissolved organic matter in the water (ie, poo and leftover food etc). As long as it doesn't jump drastically from say 7.0 to 8.0 in the matter of a few hours, Fred will be okay. Some natural deviation in pH is to be expected.
High levels of C02 in the water because of plants would actually cause the pH to plummet. If you are using C02 supplements, be sure to monitor the pH. It would be a good idea to only run C02 during the day for about 8 hours and then turn it off. If you are using a liquid C02 supplement like Seachem Excel, don't worry. It won't harm anything.