The clymer book is detailed, but its a condensed version of the shop manual. the shop manual is all you really need. i printed mine out and stuck it in a binder i keep in my work space. it can be downloaded here on the forum.
dont let it be intimidating
carbs, timing,
accel pump, and fast idle cam - these are some basic systems that you will need to learn and know as they directly effect your CB's starting and performance. I learned a lot by reading the shop manual and clymer, but i got the most help talking to members here. read first, though, so you have a basic understanding. your pumper style carbs do not have an accel pump or fast idle cam as listed in my response above.
jump right to the
periodical maintenance section of the shop manual. pg 170. do each item listed under the 3000 mi service. if you dont know how to do it, jump to that section in the manual.
bikes with mismatched parts arent uncommon at all. yours should be fine. it really depends on what you're going to do with it. if a total restore to factory is the plan, then you probably should have passed on this one.

if making a bike that is yours, to learn to ride, wrench, and have some fun on, then dont sweat it.
My 78K has a few odd parts, too...