To deal with an excess close parenthesis, first go to the beginning of the file, then type C-u -1 C-M-u to find the end of the first unbalanced defun.
Then find the actual matching close parenthesis by typing C-M-f at the beginning of that defun. This will leave you somewhere short of the place where the defun ought to end. It is possible that you will find a spurious close parenthesis in that vicinity.
If you don't see a problem at that point, the next thing to do is to type C-M-q at the beginning of the defun. A range of lines will probably shift left; if so, the missing open parenthesis or spurious close parenthesis is probably near the first of those lines. (However, don't assume this is true; study the code to make sure.) Once you have found the discrepancy, undo the C-M-q with C-_, since the old indentation is probably appropriate to the intended parentheses.
After you think you have fixed the problem, use C-M-q again. If the old indentation actually fits the intended nesting of parentheses, and you have put back those parentheses, C-M-q should not change anything.