Hi, Apollostaar, this is your first post so welcome to the forum, you have come to the right place for help! I have 1978 XS650 SE with Boyer Bransden ignition and the route I went was to rewire the bike completely - the stock wiring was so hacked about, that seemed the easiest way for me. You could take a look at my simplified wiring diagram here:
http://www.xs650.com/threads/miss-november-xs2-tribute.55057/page-40#post-632045
But to answer your questions, the safety relay is to stop the starter being engaged if the engine is running. That seems useful, so I kept it. The light checker is there to warn you if your headlamp bulb fails - if I got that wrong, somebody will correct the error - but anyway, I simply removed it. Which saved me a whole bunch of wires. The 1979 bike also had a reserve light unit, which your bike probably doesn't, the function was to illuminate the main beam in the event of the dip failing. Seems daft, so removed to save more complexity. Also, removed the flash cancel unit - your bike might not have this? - which used feeds from speedo etc to work out when to cancel the indicators. Saved a lot more complexity.
There are lots of knowledgeable folk here who will ask you which wiring harness you have and then tell you which colour to connect where to make it all work. I used to be in complete awe of electrics but having now rewired this bike and an old Triumph have come to realise that although it all looks very complex, in fact it's not. For the turn signals, all you need is a wire from the battery > fuse > flasher relay (under front of petrol tank) > flasher switch which them completes the circuit to left or right flashers > ground. You can follow these through - a multi-meter is
very useful to check continuity. Good luck!