So this is a mod_perl application? I think the issue may have more to do with non-optimized routines and algorithmic inefficiencies than just the size of the code. So, no, it is not the size of you script, but the things you are doing in your script. I'd suggest running some sort of profiler - there are many around, though I am not very familiar with any of them.

Also, if it is a web app, then I am sure 100,000 hits per day would bring many systems to a crawl especially if the code is as monolithic as you make it seem. Can you post some specifics like what you are using it for, if it is a cgi, etc? It will get you much more help.