Making good progress.  About to put my headlamp bucket back on fitted with the new voltage regulator.  Two questions 
can I just tap into the blue lead up there? I went ground to the frame under the horn. Q2 where does this big clump of wires fit? I had it behind the bucket but some came loose. Does it gotta go to slightly to the side of the bucket? 

Q1) Yes, so long as you follow the instructions in the Yamaha Service Bulletin on this subject (it's in the Tech Library).
Q2) Most of the wires are connected within the headlight shell.

Hi there Principal282, maybe you've been using a different forum thread title to discuss your resto so far, one that I haven't seen? The reason I say this is because to properly help you other forum members will need to know your model of bike and year. Also 'a picture paints a thousand words' so I'm sure it would be worth posting a couple up so we can see your current problems.  Anyway to try and assist you in general terms, voltage regulators are not positioned inside headlight bowls because there simply isn't room and they get 'quite warm' (hence reason many are finned). Try instead to bolt it to the frame (scratch paint off well to get a good earth) and then run a wire to wherever you want to connect in to the wiring harness. Ideally you do want to get the 'ball of wires' you mentioned tucked away and depending on your bike, harness connector fittings etc. these are properly located inside the headlight bowl (it gets pretty busy in there..!!) and some connections are made under the tank round the back of the frame headstock.  Remember to fit a headlight bowl rubber grommet to prevent chaffing of wires when you steer the handlebars. Best of luck with it all, Andy.