What is the way to get rid of the whispers related to declaring innovators as disbelievers, the fear of falling into disbelief when not declaring the perpetrator of disbelief as a disbeliever, and to regain peace of mind and regularity in worship?

The cure for obsessive thoughts (waswas) is to turn away from them, ignore them, and return to worship. Whenever Satan casts forth such thoughts, pay no attention to them and strive against them. You are on the right path as long as you are striving against them. As for the rule "whoever does not declare a disbeliever to be a disbeliever is himself a disbeliever," it applies to one who does not declare a disbeliever whose disbelief is definitively established to be a disbeliever. Do not occupy yourself with this, as all of this is for the deeply rooted scholars. Do not worry about obsessive thoughts; you are upon Islam and do not exit it merely by them.