It's going to be really hard to translate actual cpu usage, to a variable percentage. A percentage is going to fluxiate based on what other users on your machine are doing. It would be ok to use 50% of your server if there are only 2 people hosted on it.
I think you're actually better off with cpu minents, it's somthign a little more mesurable, and accurate.
Probably one of the best ways to figure out which parts of your site are getting hit up hard, would be to take a look at your stats. What files are accessed most, is it this 'canned script' you refered to, or something else. This may not be 100% accurate, but it's better than just knowing that one of your php scripts.
You can also check out your server logs - just FTP in, move into the log directory. Download and evulate the success logs. You may want to import to a database so you can tweak and sort, but that may also help you figure out where your getting heavy usage.
If you're regurarly hitting 50cpu min. you don't have that much you need to trim down on to get to 40cpu min. You might have luck contacting the author of your script, or a support forum associated with it, and see if there is some way to trim down on the resources it's using. For example, I know a lot of forum softwares kinda resource hogs, and a lot of people have come up with various tricks and code re-writes to help make it run better.