Sounds like you didn't have much choice except to remove the burr comb from the lid if you ever wanted to access the inside again. Bees can work extremely fast filling empty spaces. It can become a tangled mess that only a bee can appreciate. Frames & foundation are for human needs not for the bees needs.
I suggest removing the old comb from the floor. Melt it down & use a paintbrush to add a thin layer to the artificial foundations. Then install all the frames back into the hive. Don't beat yourself up over forgetting. Consider it a lesson learned the hard way & move on. It seems there is plenty of bee activity near you so I think you'll have more soon.
About honey harvest ... since I don't know anything about your seasons or pollen availability throughout the year just remember that is the bee food supply. Harvest very sparingly & only after they are well established with a large honey supply.
Good luck. You got this!!!
