Perlbeginner:

One of the great things about unix is the philosophy that a program should do one thing well, and be easy to combine with other programs to do work. For example, you can accomplish many tasks with a combination of sort, grep, cut, paste and join without writing a line of code. So if you're finding merging your programs to be difficult, you could instead tune them up such that they work well with each other.

After a brief glance it appears that the first script can work on all the files in a directory. So perhaps the second one should simply drop files into that directory for processing.

...roboticus

When your only tool is a hammer, all problems look like your thumb.