I'm sorry I couldn't help over the wiring. Your best plan in the absence of an original schematic would be to find another alternator-fitted British twin from the same year with similar switchgear (there are plenty of wiring diagrams on the internet).
I don't know to what extent you might want to modernize the electrical system - if at all. If you want an original as possible 6V system that might take longer, but running 12V instead will permit a simplified wiring scheme. A modern 12V regulator/rectifier can be tucked away out of sight (but still in the air flow for cooling).
For putting together your own wiring loom all the different Lucas coloured wires are available (in the UK at least), or you can buy multicore cable with as many different coloured wires as you need. 10 is probably enough, if you are not fitting indicators, 7 core trailer flex will do, at least as the backbone of your wiring harness. You can still cloth braid it until an original turns up (I wouldn't put it past you to come up with some clever tool to speed up the process). The layout is more or less determined by the positioning of the components, with enough slack left at the front to allow the forks to turn freely in both directions.
Or it could just be psychedelic spaghetti monster time!
It does look a bit tidier now, fortunately...
Try here for multicore, otherwise I'm sure you can buy some locally.
http://www.ebay.co.uk/itm/10-CORE-AUTO-CABLE-1-0mm-16-5-AMP-CAR-WIRE-3-METRES-MULTICORE-AUTOMOTIVE-3M-/251125011570?hash=item3a78379472:m:mv72-OMYcFDw-e3hTOr4Tmwhttp://www.ebay.co.uk/itm/13-CORE-AUTO-CABLE-3M-1-5mm-21-AMP-CAR-BOAT-LOOM-WIRE-3-METRE-THINWALL-1-5MM-3M-/261266757164?hash=item3cd4b6562c:g:Ho8AAMXQ2dBSD4AMAs for the exhaust pipe, it looks like it's not far off. The pipe I bought for my Not a Fury was a poor fit (sold to me as such), sorted by gently bending the relevant bracket to line up with the mounting stud until it **did** fit! You could also open out the hole in the pipe bracket just enough for it to slide onto to through-stud properly, and make sure it's covered by a heavy-gauge repair washer, but something tells me you wouldn't do that.
Hopefully the pipe will then line up properly with the rest of the bike, though if you have to fit a spacers between the bracket and the frame you will have to fit a longer than standard 3/8" CEI/BSC through stud, you can get these in stainless steel here:
http://motalia.com/index.html If that were my clutch cable I would simply trim the outer cable back to expose enough inner to reach the actuating arm, assuming the cable as a whole is long enough (I wouldn't trust myself to re-solder the nipple). If you had to destroy the ferrule on the outer cable to do so, a carefully slotted new ferrule could be placed on the shortened outer cable end.
A.