As soon as your system is up and running, you might ask yourself what to do next? The real system documentation is the MinSoC document. It gives a thorough insight into MinSoC, its goals, design and ideas. It helps you to better understand the system and can give you a good idea of what to do next, after your system is up and running.
If you want to know how the OpenRisc processor is implemented internally, the best you can do is check or1200 specification on or1200 page of the OpenRISC project. However, this will not explain to you how the instructions are implemented, neither does the architecture manual found under Architecture of OpenRISC project. They only give you an understanding of the design and its global picture.
To understand the implementation details, you have to read the source. You will be mostly interested in or1200_alu.v, though or1200_cpu.v and or1200_ctrl.v might be important to have the bigger picture.
However, in order to do so, you have to understand HDL very well, so please go first to the following links:
Then you have to read the available documentation of OpenRISC: First, the architectural manual, then or1200 implementation specification, and possibly the supplementary programmer's reference manual (specially if you want to include new instructions).
Finally you can go to the sources. Be sure to use special tools to help you navigate the code. This link can help you to install one possible set.