If I were you I'd do pin-pulls instead of doing deads off the floor. But as for squatting, I'd just take a break from all variations/styles. If your doctor told you your knees are bad then don't do any movement where you put pressure and stress on them, ESPECIALLY IN A FULLY BENT POSITION. Pin-pulls will be sufficient IMO. Your knees barely play a role in the movement, you'll continue to strengthen your lower back/posterior chain, and pin-pulls are just plain fun. I'd also throw in some t-bar rows or pendlay rows to help with developing thickness in leu of deadlifting.
Keep your calories up. Utilize the energy you aren't using on squatting and deadlifting for something else, like benching or pressing. Just make sure your workouts are still intense and you shouldn't have to worry about it. If anything just lower your carb intake on the days you aren't training.
I hope this helps you out, brother. Stay positive and keep pushin' forward.
"There is no passion, without some obsession."