Back min the olden days engines didn't even have timing marks. Put the piston at TDC ar rhe end of the squeeze stroke/beginning of the bang stroke. Adjust valve clearances. Go ride. If the engine runs right, don't worry about it.
I feel like writing a big, nasty, whiny sob story right now, because this bike and this whole situation is really getting on my nerves big time! But it would be a waste of time, so I'll refrain. Thanks for the replies people. I will do a compression test. Also, I already disconnected the throttle cables. But it's fine as I was planning on doing a carb sync anyway, and I bought a tool (Morgan Carbtune) with which to do that. I'll let you guys know how it goes.
EB1156: I rotated the crankshaft around several times and the T mark didn't line up when the dot on the cam sprocket was where it should be, OR when the dot was 180 degrees off. But thanks.
If you're getting all emotional it's time to pull on your big-boy panties and GET 'ER DONE!
Have you read the instructions? Have you been to http://www.ex-500.com/ ? It's a machine, not a woman.
It's a simple matter of following the instructions step-by-step. Always is. Most common mistake people make is not reading and following the step-by-step instruction. I expect there is some minor detail in the instructions that you are over-looking. Once you figure it out, it will seem so obvious you'll feel really stupid. Take a break, relax, kick up your feet, peruse the shop manual like it was a Playboy, you'll figure it out.
Don't make the mistake of compounding problems by starting another repair/adjustment without completing the first repair/ adjustment. That's the second most common mistake people make.
The Morgan Carbtune is the best synchronizer available. Good choice. (I use a homemade tool made of clear plastic tubing, a board, and using motor oil for an indicator. Cheap choice.)
So I adjusted the valves to spec, did a ton of other maintenance, and put everything back together. Have been riding the bike for a few hundred miles since then and thus far it has been one hundred percent perfect! I love this bike - so much fun on a twisty road, and an awesome commuter at the same time. It seems like I did indeed catch the problem before it became serious. Thanks for the input. Look for pics of my new ride in the "off topic and other bikes" section in the near future.
If you think the 500 Ninja is great, wait until you ride the 650. I know several people who started out or worked up to a 500, then went to a I4 sport or sport touring bike or three, then to the 650. Not that much different in the twisties, not so much top end, but the maintenance is nothing costwise or timewise compaered to the I4s.