If they both seem happy sharing, then no harm. If Bobo is skinny or sick from being a stray, I doubt a couple of months worth of kitten food will hurt him. You can feed kittens regular food, they just will eat more of it. If you really want them to eat separate food, feed them in different rooms, leave the food down for ~30 minutes, and then clean up. They will learn the new schedule pretty fast.
And if they both like to use one box, why force them to change that? As long as neither one is upset by sharing, then I would encourage it.
I have two kittens, sisters, and they share everything. All my cats have always shared, and have never had a problem. Even the ones who didn't love each other managed to tolerate each other at dinner time.