I'd taste them, try not to disrupt the pellicle too much. Then you go from there, maybe age them longer if needed. Or if its where you like it bottle them, or blend them, or rack them on to fruit.
Take sample & taste it, that krausen on top may smell a bit different from your beer. I've not had any issue with Oregon cherry purée, but there are many places to pick up an Infection. I'd rack it to another carboy see if its still funky with out all the dead yeast, cherries & nibs.
I make a chocolate coconut porter & I didn't have any issues with carbonation. I've both bottle conditioned & kegged. Maybe a bit poor on head retention but not too bad.
Kumquats are used just like orange peel, use them whole & toss them in @ the end of the boil or in the secondary. I'd do both just like your thinking, but I'm not sure about the amount? I would compare it to orange peel by surface area so 3-4 = 1 orange? Guessing here, I would start with about...
I've used it for a lambic not a rodenbach clone, it was a year before I tasted it & still need more time. I also like to add dregs to mine for complexity. If I was to go with a blend without dregs I'd use ECY20 that stuff is awesome.
Edit add; I normally leave my lambics on the trub but I rack...