if i get the circuit modified ( the blackbox)
I misunderstood your first post. The "blackbox" is something that already exists and you're trying to get data out of it?
- After I get my signals ready, I need to do all kinds of processing: frequencies, energy, stability, etc...
and get the output to be at 1ms, could i do it with arduino??
No one here will be able to answer your question. There's too much information in your head that isn't in your post.
if i could link the arduino to a program made in c#. how could i even do that?
The Arduino is presented to the computer as a standard serial port. Your C# application interacts with it through a serial port.