Debugging PHP Script

I have an enormus amount of code that makes use of mysql, and creates and deletes files. It's a shell script that is run every 3 minutes by a crontab. The problem I'm having is that unpredictibly (and very far apart) it'll give an error (for 30 seconds stragit) "Invalid file handling resource". But because it happens at unpredicted times, and usually several hours apart I cannot figure out what's wrong with the thing. The system isn't busy, nothing's using it's files, etc.. Checking logs by crontab shows it doesn't happen at specific time intervals. So my question would be, is there something that'll help me debug my script? I'm flat out of ideas, and I'm running out of Dr. Pepper (soon I'll be useless). Any help would be greatly appreciated, Thanks, Chris