how do I group a large drawing of about 1000 'pencil marks' in acrobat pro mac

This is only possible using a script, and all the annotations have to be on the same page. You would also lose all the comments you made, colors you used, etc., for all of the annotations (except for one). But there's a much easier way to do it. You can export the comments data to an FDF file, and then import that file into the other PDF, and the comments will be recreated in exactly the same locations and with exactly the same properties as in the original file.