Sorry I hadn't spotted this topic earlier, but I wrote the original article in
MZ Rider that
http://www.sweller.co.uk/mz/mods/mod_12vreg.html is based on. (About 20 years ago! - good to see people are still reading it).
You're nearly there - connect the red and red/yellow wires together through a 15 Amp fuse. The original mechanical regulator had an 'over current cutout' across these two terminals in case of a short circuit, the fuse will have the same effect.
Hopefully, once you've connected these wires, everything should work.
If you look at this wiring diagram:
http://www.sweller.co.uk/mz/electrics/wir_tz12.html you'll see that the other end of the red wire connects to the battery and the fuse. This is the 'output' of the alternator, which comes into the regulator on pin DF (red/yellow) and passes through this cutout. Pins 61 and D- measure the output voltage of the alternator and the regulator varies the voltage on pin DF to keep the output voltage constant.
Hope this is of some help.
Norman