Maintainability is exactly the issue here. My architect freind says break it up so each piece is small and easily digestible w.r.t. function, even if this means calling multiple scripts to do the "job". My view is to have it all in one place so I don't have to chase around multiple files/locations to figure out what the job is doing.

I don't think the two are completely at odds. Even though my script ended up longer than I expected, I did:
- use subroutines to avoid repeating the same constructs
- commented liberally, since I and my admins are all relatively new to perl
- wrote a pretty comprehensive perldoc, that describes what the control file looks like and how to call the script with the control file and the available args.