This will be painful, but I think the best start will be to write documentation and tests. That should expose whatever unities may have survived what sounds like a normally haphazard development.
You probably have three major independent chunks. The GUI/event mechanism is probably easy to encapsulate, since it depends on Tk and has a clear interface in the event handlers and dialogs (or whatever). The second and perhaps third chunk is the control mechanism in the "batch file" generating and parsing. The other third is the interfaces to external tools you call.
That leaves out utility modules that you will probably need. You say there are lots of global variables. Trying to limit those to smaller scopes will go a long way towards exposing closely related code. Those that are truly global become part of your configuration module.
I hope you're granted time to do this right. Have fun!
After Compline,
Zaxo
In reply to Re: reworking a large program
by Zaxo
in thread reworking a large program
by gri6507
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