Generally, in ACL, you would use the Declicker to remove pops and scratches.  Obviously, it may not completely remove really bad scratches.

From what I can tell, ACL does not have a manual editing tool.  I do know MMM does, however the file must be in WAV format.

With this you can reduce or completely eliminate a large scratch/pop, however you will also cause a drop-out in the sound as well.  You'd just have to decide which one would be easier to tolerate...a pop or a drop-out.

Or, you could cut and past a similar section and paste it over the pop/scratch. Then, the repair may be less apparent.