If you have the option i'd look for a physical therapist and ask his opinion, you need to find out exactly why you have pain during those lifts, then find corrective exercises you can do to address the problem, your form could be off or you could have an injury.
If you can't find or correct the issue then find replacement lifts that you can do. Alot of people can't back squat or deadlift, but usually there's a varation of those you can do, like a bulgarian split squat and stiff legged deadlift.
Also there's no such thing as tone muscle and bulk muscle, muscle growth is muscle growth, your size depends on how effective your diet,effort, programming, and rest are. High reps builds muscle, heavy reps build muscle, metabolic training grows muscle, eccentric training grows muscle.
