Sounds fun , im also doing the same but my bike was a wreck.
I have the clymer manual and think its very well detailed TBH.
Regarding the official kawasaki manual , i have no idea how it is.
Help wise you seem to have everything covered , taking the bottom of the engine apart is pretty easy with the right tools , this is my first bike i have every stripped down.
But the tools are expensive , i bought a crank case splitter , fly wheel puller , 8mm t handle spanner , clutch basket holder and now need a blind bearing puller.
Yes i know a waste if you use them only once , but if you plan on building more bikes then they save you a huge amount in the long run.
Im UK based so dont have access to sand blaster and his amazing engine skills.
Depending on what your going for i would get the engine vapour blasted for thar new look , and do you want it original looking?
Im going for fully custom and will start a thread next week.
Also please start a thread as we all love progress pics