The "finished" paper always takes effort; sometimes it takes sweat and tears. But never fear to make changes, major changes during revision or minor changes during proofreading. The best papers are those that we give our best thoughts to and those that show we can reject our less-than-best writing.
Proofreading is the very last step in preparing a final draft. Just because it's the last step, though, don't assume that it will go quickly. Sometimes it take two or more additional "passes" through a paper to be sure you've found all the remaining typographical errors, misplaced pieces of punctuation, or inaccurate words.