'94 Kawasaki ZZR600: Electrical issues

first post here, be gentle 🙂

I have an (presumeably) electrical issues with my ’94 Kawasaki ZZR600 (ZX6). Two weeks ago, I was ready to go to work when suddenly the bike died on me, all electrical power was gone. This happened right after starting the bike. At first I thought about a short/blown fuse, but after waiting a while and turning the key again, power was back. Weird. Fast forward to a trouble-free week later, when the same thing happens, and the bike just completely dies during riding, on my way to work. On the way back home, the bike stuttered violently and rocked me back and forth on my seat. I avoided the highway and take the scenic route home, but the bike seemed to lack power. Also, when the bike was running poorly it almost threw me of the seat, and I could clearly hear a very loud bang coming from my exhaust, similar to when incomplete combustion occurs (running on three cylinders maybe?)

And then this happened

Back home, I expected all my wires and lo and behold….every connector between regulator/rectifier and alternator have MELTED.

More Pictures here

So in short, symptons

1. Starts very poorly, but (used to) run fine afterwards
2. Dies completely (loses all electrical power), only to come to alive again
   a few minutes later
3. Stalls during riding
4. The bike violently rocks me
   back and forth on my seat, like the ignition is completely off
5. Connectors between regulator/rectifier and alternator are fried, reg/rec unit and junction box are toast

What I’ve done soo far

1. I’ve checked my fuses and measured the battery voltage before, during and after starting the bike, all seemed fine.
2. Inspected the regulator/rectifier and junction box, by using the method described in my Haynes manual. Both units are defective. The alternator itself is fine.

Questions
Since I’m curious as to what has happened and what’s the best option to fix it, I now have some questions:

1. Regarding the cause of all this: I suspect that the reg/rec unit has died, so the alternator couldn’t get rid of the higher voltage, thereby melting wires and frying components. Does this sound plausible, or is there another explanation? Maybe the problem originated in the old wiring and connectors?

2. Why didn’t any of my fuses blow? Aren’t they designed to prevent exactly this kind of damage?

3. The connectors between alternator and reg/rec unit are gone. The junction box also took a hit. I have yet to check the other electrical components, but can I expect more damage?
4. I’ve already found a new reg/rec unit and alternator and plan to replace the affected wiring and connectors, but would this be sufficient and a good way to fix my damage or is there something I could do better?

I realise this is a long post so thanks in advance for sticking with it so far, and hope you have some ideas to help me. Thanks in advance!