Well after four and a half months, we’ve reached the point where Clover is no longer tolerating being locked up in his pen at all. He used to be alright with it, not exactly happy, but he wouldn’t make a fuss when I would lock him up to sleep. However, as I said, that’s unfortunately no longer the case.
He’s been protesting a ton for the past week, by either making a complete mess of his pen to demonstrate his boredom (rearranging everything, flipping over his box, scattering his folded blankets, etc) or by grabbing and chewing the cage bars and making a ton of noise to say not very content. He started doing this a month or so back, but I solved the problem by either covering up the bars with cardboard or hanging a blanket over them, but he’s now just slipping under the blanket to have a go at them.
While I could just keep fighting him on this, I feel like the more ideal compromise for the both of us is to just let him be a free range bunny, but instead of having access to my bedroom, the bathroom, and the TV room as usual, I’d just give him access to the bedroom. And he’s certainly earned it. He’s totally litter trained, only ever having tiny accidents in his pen (and even then only dry poops, never pee), he never chews on anything, even when I accidentally leave wired headphones on the floor, and he’s respectful and doesn’t make a ruckus, the most noise he ever makes out of the pen is just from excited running and binkying. My main reason for wanting a pen for him is so I have the option of locking him up if I need to, and at night I like to know exactly where he is in case, gosh forbid, some emergency happen at night and I need to grab him immediately. But that’s more to my paranoia than any realistic emergency that could happen. 
So this leads me to ask. If I wanted to transition Clover to free range, what would I need to know about it? I’m guessing it’s almost as easy as just having a normal cat or dog, along with bunny proofing, but is there anything else I should know? Right now the pen I have set up for him is cage walling, plastic to protect the baseboard, and vinyl flooring. I know rabbits like having a little corner to themselves, so should I remove the cage walling but leave the vinyl flooring to protect the carpet at the litter box area and keep it clear that that’s his little space? Thank you!