Start tracing the ABCs in the air with your toes daily, do the alphabet forward and backward - that’s one of the best stretches my buddy used to come back from an Achilles tear this past year. Knees is likely from muscles tightening up, or perhaps hamstrings weakening if enough time off has passed.
You need to find some training that excites you - the best method is the one you will execute faithfully and with true intent. Your bench is poverty compared to your lower body lifts, and it sounds like you may be a little beat down - if it interests you, consider a 3 day/wk bench specialization routine. This likely pulls back on your overall training workload & time in gym for now, lets you improve your biggest weakness, & is something different. Example:
Tuesday
ME Bench
Thursday
ME Deadlift, DE Squat (rotating efforts weekly)
Saturday
DE/RE Bench
This is just an example, but also consider part of why you aren’t getting stronger is that you aren’t eating enough to fuel your training! There’s no one size fits all for calories, but the fact you brought it up means you know you’re coming up short. Food is your power & your energy. Without food and sleep you will just spin your wheels.