Re: motor out of box,,, any cause for alarm
A) That rear mount stud can be replaced with an M6x1.0 of the correct length.
B) I wouldn't worry about the condition of that rubber boot for now.Make a mental note to replace later with a decent wire and cap, but it'll work for the time being.
C) There might be a little play in the engine sprocket. Again, don't worry about that for now.
D) Point the clutch arm straight back, then try to push it towards the motor (right under where the carb goes). It'll be really hard, but it'll push a bit. That's your clutch. If the clutch arm is swinging completely inward with no resistance, then you have a problem, probably the bucking bar or clutch ball missing. We'll deal with that after you make sure about the clutch arm.
To replace the plug wire, unscrew the wire from the CDI. It might be epoxied in there, but it'll come out. Replace with a 7mm wire and cap, which you can get from a variety of local places (auto or bike parts stores). If you get a standard automotive plug cap, you'll need the little screw on nib for the end of the spark plug, but if you're replacing the wire and cap, you may as well do an NGK plug at the same time, which will come with that. If you want to keep the threaded top plug style, ask for a wire from an old air-cooled VW (Beetle, 411, Ghia, whatever).
The big thing I found with my first kit is to replace the hardware that holds the chain tensioner bracket to the chainstay. The bolts I had were so soft that their heads broke off before I could get them anywhere near tight enough.
If you don't already have a method for chainbreaking, get one. Harbor Freight sells a cheap chain breaker for the big chain that works, as long as you sand down the pin. A bike chain breaker will likely bend before it pushes the pin out. Lots of people do it with a hammer and a nail with the tip cut off, but that's not my style.
Check the inside of the tank for trash - paint, bits of metal, squirrels. Shake some ball bearings around in there to get the loose junk out, and flush it out with a little gasoline (before installing the petcock).
You will need to sort out the front mount after the bike comes, so that you know just what you need for it, if anything.
Take one of the head nuts off, and see if the studs are 8mm or 6mm. Torque all the head nuts (in an "X" pattern) to 50-70 in-lbs for 6mm, 150-180 in-lbs for 8mm. (If you don't have a 1/4" drive torque wrench, they're cheap, and you want one.)