I'm sure others will point this out, but "lines of code" is both hard to count (especially in Perl because of its potential density) and not a particularly useful metric for anything (like scheduling).

However, if I were counting lines of code for comparison, I'd remove comments and blank lines, as it's the same code without them, and probably run it through perltidy or some other formatter to standardize the format. If you're estimating schedules, you should be able to apply some factor to compare uncommented code with commented code.

You may want to look into other metrics if you're actually using these numbers for anything other than curiosity. Robert C. Martin proposed some OO ones for C++-like languages in one of his books (sorry, I don't have the title); "cyclomatic complexity" takes into account the number of decision points in your code; there's also "feature point" and "function point" metrics which have the advantage of (theoretically) being computable before you code.

As far as whether your program is large, I'll let others answer this better, but it seems pretty large to me.