Whew, that's a lot of questions but I'll give them a shot.
One of the best places that I've found for Zen parts and a lot of other things that you need is at
http://www.gizmomotors.com/ . I just placed an order with him on Monday, fast service and it's hard for anyone to beat his prices. He does have everything that you need to whip it back into shape.
The cooling jacket and associated parts can be cleaned upwith something like CLR as you have a lot of calcium or lime build-up in there.
Yeah, I'd replace the cable but keep it around for a spare. The stuffing tube is no biggie but it might cost you a hair over a buck to replace it!

It's a little hard to see if the Zen has has any work done to it from the shots. A quick and easy way to find out generally is to see if anything was done to the exhaust port. Externally they all pretty much look alike. The numbers on the bottom of the case are from the factory.
Walbro carbs are very good and the industry standard for Zenoah's, Sikk's, RCMK's and every other manufacturer including yard and garden equipment.
OK, now to the strut and rudder. I don't know for sure who made it right off-hand. The strut is mounted correctly although it looks backwards but you want the sharpened piece forward. The drive dog then prop will balance it out in the looks department when it's tossed back together. Yes, the previous owner either tweaked on the strut or bent it some other way (dropped it?). You can straighten it or the foresaid owner bent it to the right as a quick way to offset it to the right to help compensate for torque.
The cowl locks work well but have seen better days. Those are Aeromarine pieces and come in two different styles topside but those bases are the same.
I think that I hit on most of the questions so mow I've got one for you. How far are you going to go with the rebuild? If you keep the stock strudder (strut and rudder) I'd be doing something about the Z bend in the rudder linkage as you want that as straight as possible.
Go through the Gizmo site and you may see a lot of other things that you's like to update or make better.