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If you are going to a smaller battery then you will need a geared starter - the Valeo or said to be better Mitsubishi (from some BMW electrics mob - search the site). Also wire the starter relay so it goes directly to the battery and avoids the key switch.
and add a relay for the light and horn.
I would throw away the wiring harness - it is 30 years old, has twice the wires needed (Guzzi used a universal wiring harness that has a pile of wires for police/military radios etc). Unlike a car wiring harness, a motorcycle harness moves and will inevitably work harden. Also Guzzi was pisspoor at doing grounds - it is good to have a single ground point that everything grounds to. Spiral wrap protector does a very nice job.
If you stick with the bosch system which is simple and robust but underpowered I would stick with the separate regulator (although I would replace it with an electronic one) and rectifier. They are easy and cheap to fix anywhere where if an integrated box goes tits up your stuck. I would replace all bulbs possible with LEDs to bring the power requirements down + maybe HIDs now that they can be had a reasonable price.
Buy a good crimper - soldered joints actually are more likely to fail as they create a stress raiser in the wire as the solder is wicked into the wire. It took me a while to believe this to be true - I used to do both because I didn't trust the mechanical or electrical connections of a crimp but I was wrong. The automotive connectors versus the old molex/amp ones are much superior but not so easy to get for you and me.
Also use dielectric grease sparingly - it is properly conductive grease and can cause shorts. White grease is a better bet and thats what the automotive world uses for everything but HT.
ChrisR