reg/rec

If your bike is standard it will be a single phase alternator. There is a very simple way to decide though. If it has two wires from the alternator it is single phase, three wires means three phase.

You can disconnect the rectifier and both zener diodes if using a modern style reg/rec. I would leave any red (ground) wires connected. Then just connect the two/three wires from the alternator to the same coloured wires (probably yellow) on the new reg/rec and the red wire from the reg/rec to positive terminal of the battery (which will be ground if your electrics are unaltered) then the black wire from reg/rec to battery negative. It would be a good idea to use an inline fuse in the black wire. 

I'm not sure how the ignition warning light is wired on a Mk 3 but there is a good chance it won't work after you fit new reg/rec. Alan Osbourn sells a better version that will work. 

Ian

Ian, thanks for the mention above, but there is some 'casual' inacuracies (rubbish spelling NO spell cheker) in your words. Three wires from a Lucas type Stator does NOT mean 3 phase. It would appear that Lucas in the 60s when they made 6V RM19 alternators they bought the worlds supply of GRN/BLK, GRN/YLW and WHT/GRN these colours have been used on RM19 and High Output Single phase (but still with 3 wires). As well as 3 phase (where identification of the three wires is not done) The only test for 3 phase is to look at the pole pieces, 6 is single phase, 9 is three phase. The rotors are all the same., (As far as phasing is concerned).

When changing to a new style reg/rect you must remove the original rectifier and Zeners. Do not connect the reg/rect wires to the battery (although this will work) it is far better to feed the reg/rect into your bikes wiring thus-RED Positive-to Earth. BLACK Negative-to the BRN/BLU that was fed from the old rectifier and is a feed into the bikes wiring. Do not double up at the battery, as eventualy you will miss a wire, break a wire etc. Is is always best to have one decent wire feeding the battery into the fuse and bikes wiring, RED to Positive BRN/BLU to the negative with no errors or guesses.

The MKIII Assimilator  should work unless faulty, might give some odd results if you did have a real 3 phase system. Yes I do have a couple items that can be used as monitors for electrics and charging.

I missed a point here that needs clarifying, you say you would like to fit an 'uprated' reg/rect in place of the Rectifier-Zener. As far as the battery is concerned there is very little difference between these two set ups. They both control or limit the maximum battery-hence charge-voltage.

Rectifiers are cheap and very reliable, but Zeners are no longer available, Lucas stopped making then in the 80s the fact that so many are still in reliable use confirms their suitability and reliability for the job. Any so called Zener diode you now buy for this job will be of inferior parentage-do not use. 

So the modern Reg/Rect (I sell one of these and can test them) is a very neat easy to fit and modest in price item. It has a good final voltage, so in that area can possible be better for limiting battery over volts, but they can fail more often than one would like. So there is nothing wrong with the 'old' zener system, but it might be neater and tidier to fit the new 'gubbins'.