The Multichannel Analyzer and it's supporting software is probably the most difficult part of the project. Open designs for them are fairly lacking and commercial products are fairly expensive. While not demanding, care will need be taken when dealing with high voltages and nanosecond length signals.  Signals will be fed to the analog front end where they will amplified and where the protection circuitry is located. Then they will fed into an ADC connected to an FPGA, which will handle all the signal processing. This is all controlled by a microcontroller which will also communicate with the host.