Test Tool for our environment

I need a litle bit support or ideas to start a new project for my company.

The tool must be a test tool (outside) of an IDE.

The main scenario is:
it has a file as input and it has a lot of file as output. The main programm is composed of a lot of java, bash and other programming languages modules.

The input file has a variable number of parameters ( from 100 to over 1000).
Parameters can influence only one of the main moduls, but also more modules, and more variables together can change completly output files.

Every three months we have changes to made to the whole system, and we would to have a sort of regression test, but also we would have the possibility to take out the code that we didn't need.
Other thing is, They're are more than 15 people that work with the system, and we loved to have a centralized tool to introduce this regression configuration.
Plus we don't have the control of all the possibility of input files: this means a customer can send us a new input file, with a new configuration, and we have to check it, and eventually configure this new case in the test tool(so the next time we don't have to check it an other time)
An other problem is that, we become over 1000 config files a day.

We don't now what is the best thing to do:

a. start develop a tool that check's over one of this module, and after aplify it to the other modules

b. start with only integration test with the main program

c. Other?

Has anyone an expirience of a such system an an idea how to start?

Personally I would chose a) becouse it is a litle part and give me sooner feedback, than b). But i think they are other possibilities that I didn't know.

Tank's in advance.