Hi ideel and welcome to the forums!
I will try and answer your questions. I am assuming you are basically just building a heliostat, although your wording makes me wonder if you are doing something a bit different.
- can a mirror with some photo-diode on it be enough or have the tracker and the mirror working individually?
I have never tried this, but I have seen at least one person who has. http://www.heliostat.us/
The photo-diode isn't on the mirror though. It is basically in front of the heliostat in line with the target so that it picks up the reflected light instead of the sun's light.
- what Micro-controller to use?
If you want to reuse the code on this site you are probably better off sticking with either the Arduino Uno, or the Arduino Mega. The Mega is best if you want better accuracy, which you might need if you are doing something with astronomy. There are of course plenty of other microcontrollers out there, but they most likely will take more effort on your part to make them work.
- what kind of motors/servos?
Again, if you want to reuse the code on this site, you are better sticking with stepper motors. You will of course need a driver board to go with each stepper motor.
- how to transfer data (most cheapest way possible) over 30meter/100ft through USB 3.0?
I personally don't have a whole lot of experience with wireless communication other than a bit with XBee wireless. The XBees are fairly easy to set up, but they aren't necessarily cheap. Alobo posted some stuff on the ESP8266 which seems promising. http://cerebralmeltdown.com/forum/index.php?topic=854.msg3348#new
I kind of doubt that they would reliably operate over 30 meters without maybe adding an external antenna, but they are fairly cheap.
It also serves as the microcontroller too, although like I said earlier, you may have to work through some more issues when switching to another microcontroller. Alobo may already have everything worked out though I'm not sure. I haven't had the time to experiment with one yet.
Some of your choices should also take into consideration how much time you have to work on this project.
Hope that helps!