I had similar problems with my 750. I got an online manual from here which helped a tonne. http://www.yamahatriples.com/files/5613/2786/4749/Yamaha_XS750_Service_Manual.pdf
If you pull the seat/tank you should see the three coils. The cylinders are numbered 1-3 from left to right when sitting on the bike. The coils will be mounted in a similar orientation ( the farthest left for cylinder 1 and so on ). There are a few ways to make sure the wiring running to the coils is done right, each should have a red wire and then either orange, grey or yellow. From what I remember the wiring diagram in the manual is not much help in this department. I recall unplugging all three plugs leading into the coils, taking a spare spark plug and plugging it into the lead from the #1 coil and resting it against the engine, then trying the each plug leading into the coils until I could see spark when pressing the starter. Repeat for #2 cylinder and by process of elimination you will have the #3 cylinder sorted.
As for timing, pull the left side cover from the engine to see the timing unit and governor. On mine there was three screws holding in the plate that the triangular black box is on, which is essentially your pickup coils for each cylinder. Loosening the three screws will allow you to rotate this plate. The trick is the timing marks are on the governor plate behind the gold plate, and it has only one position on the crankshaft. This makes it very tricky to do without a timing light. The manual in the link above only has points timing however it has good info on timing mark meaning and factory specs for advanced and retarded settings. I had to do a lot of trial and error along with reading in forums to get it sorted sadly, so I hope if you still need this info this steers you in the right direction at the very least.
mK