I wouldn't worry too much. A while back we were building a thread on the less than spectacular things we do. Funnily enough, you are not alone...
I have a cap in the same condition as yours, and will be interested in seeing the results of your repair.
You have a fair bit to do to your bike, but the main lumps are in one piece, which is a good start. How do you plan to use the bike? If you are going to use it regularly, then you might take a different path than if you plan to build a show bike.
When you get to the motor, as well as the usual stuff, consider fitting either larger diameter, stepped studs or helicoils / inserts into the head (the originals pull out as you tighten them) and make sure the crankshaft oilways are cleaned out with wire - not just air. Blockages are the main cause of thrown rods.
Draganfly do full sets of nuts and bolts. Pulling them apart seems to always mean losing / stuffing up some of them.
Bennet Longman does 12V Alternators - made from GPz items (see knowledgebase).
You can get the exact info about how your bike left the factory from the club registrar.
BTW, I don't think the big battery on the "one day" photo is correct, so don't chuck your battery carrier out if you have a smaller one.
I also do think that the rounded flat steel bracket (posted earlier) is for an aircleaner.
'51,'56 Squares, '48 VH, '27 Model C, R67/2, Mk IV Le Mans, '06 Super Duke and Ariel projects.