Check out our Read Only Tech section, there you will find complete wiring diagrams, both factory and a "simplified" version done by one of our members. There is also a thread there where you can download the factory service manual, etc.
Yes, as Jeff said, I would start with getting spark on all 4 cylinders! There are several things to look at! As Jeff said, look at and disassemble the spark plug caps! Then unscrew the ends that go into the coils and look for green inside the coil, they get corroded in there quite often. Cut about 1/4 inch off the end of the plug wire before reinstalling and push the rubber o ring on the plug wire up away from the end a little. Those O rings keep the wire from vibrating loose from the coil. The TCI unit may also be defective, they are known to have problems.
As far as cam timing and whether or not the cam is in backwards, consult the official Yamaha service manual for this information, or, there is a great video out that you can purchase from Damon Ferraiulo concerning complete engine rebuild...
http://www.venturerider.org/forum/showthread.php?84030-DVD-of-1st-gen-motor-amp-carb-rebuild-process-purchase-info
His videos are extremely informative!! They are for the VMax motor but it is the exact motor except on the heads the valves are bigger and the cams are hotter. The assembly, to include setting up the cam timing, and which way they go in will be on that video.
Good luck and we hope we can be of assistance to you, just ask, eventually you will get an answer, and usually it is the right answer!!