Lots of good info and questions from the responses here. I might have missed it and some of your info is different than mine on region and pond equipment. I think I might look at this one a two prong approach.
First up - Aeration. I don't have aeration in my pond yet but will be an addition as we get power at the property in the future. Did you do anything special on startup like...removing the heads and cleaning the gunk off of them? Again, I don't have this option in my pond but have read some of the posts on PB that the heads need to be cleaned up annually to keep them on good shape.
Second up - Fish. Depending on your goals (Big Panish, Balanced, or Big LMB) your stocking might be different and I would hazard a guess that if RW's were known on the remaining fish population responses to what, if anything, to add would be different from many people here. Next time you fish, take a tape measure and a scale with you to measure up the fish you catch (Panfish and LMB). If you post the length and weights of the fish you catch in the thread many of the people here can help you with RW's if you don't know how to do it.
I agree with the fish kill perhaps not being the worst thing that has happened on the pond and actually might be a good thing for you and the remaining fish. Sucks to lose them but at the same time the fish population needs some help with removal of fish to keep it in balance. Several posts on the PB forum include removal of 10-20lbs of LMB culling per acre per year. What you noted in your original post falls right in that spot.
Things to keep in mind:
Dye will darken the water to help with weed control. It will also limit the plankton bloom in the water (bottom of the food chain for your baby fish). It will likely also lower the overall carrying capacity of the pond as there is a more limited food supply from the bottom which translates through the pond to the other fish (my opinion).
Pellet Feeding the fish will help promoting the fish that eat it directly and the fish that eat those fish indirectly. I don't know if this offsets dye use completely but it definitely helps.
This fall would be a great time to check the length and weight of the fish and post some info on what you are seeing. Stocking suggestions will be much more accurate with additional info. Personally, I wouldn't add any more LMB without knowing some RW's on the existing population. I'd bet if the RW's of the existing populations came back at 75-95%, 95-105% or 105+% stocking suggestions would be different from any poster here.
Good luck and welcome to PB!