Thanks for the reply. I went through the tank again yesterday and cut off all affected leaves. (mainly the anubia- they are nude now LOL) Flipped over the affected rocks again to bury the stuff alive, Used my gravel vac and a brush to get as much of it off the driftwood as possible (this is a 40lbs piece of wood in this tank anchored to the bottom of the tank so it's not going anywhere). Against my best judgment I added a couple SAE's (they tend to be lazy fishfood/plant eaters when they get older), but I found them both dead today!! Maybe the heat or PH shock? It hit 85F in the tank today and the fish are breathing quite rapidly, but not at the surface. I also added about 20 Amano's and they are doing fine. Also have 35 cherry shrimp on order. I figure the more to eat what is left the better.
One thing worth noting is that the plants havn't really ever pearled. Well, maybe the java fern a little. The only time I get good pearling is when I change the water. Perhaps I should get some riccia in there to use as an indictor plant? If the riccia pearls in the tank that should mean I have enough co2- no?
I recently decided to discontinue using the PH controller and plug the solenoid into the light timer. I have a bubble rate of 1.4bub/sec which is a little slower than when it was automated, but gives me a ph of around 6.6 in the late afternoon according to my probe with all other electronics off. My PH test kit is also saying about the same thing so hopfully the C02 is dialed in now.