You have not provided nearly enough detail to be able to help you.
What is the purpose of the mini din to USB cable - is it something specifically manufactured for your "indexer device". What is it intended to connect to at each end? How are we supposed to know?
You need to post a link to the datasheet or user-manual for the indexer device.
What is the intended role of the USB Host shield?
What is the purpose of Visual Studio C++ - that is not the normal way to create an Arduino program.
A diagram of how the proposed system is intended to work would be a big help.
...R