Lots of good advice here. I think I would approach your problem something like this:

• You say the system contains a lot of scripts/programs. Document the behaviour and create test cases at this highest level. Feed it data in various ways to get an idea of what the programs do. It will probably help you getting a good system understanding.
• Make sure it runs using strict and warnings. It will probably give you quite a few errors an bugs to fix. Fix them, hopefully without breaking anything. If you do, the tests will (maybe) tell you, but don't count on it, because you still don't "know" the system and have probably not created a complete test set. But when you're done with this, you will have a lot better code quality.
• You're gonna change a _lot_ of code, so version control is probably very useful.
• Get rid of the HERE docs to make it easier to read and refactor code. Boring but uncomplicated.
• Get rid of the globals. Labour intensive.
• _Now_ you're ready to start refactoring for real :)

/J