When the intake valves closed, the cylinder would be at BDC. It takes 1/2 of a turn to get back to TDC so that the TF would show.
Yes, as soon as the intake valves were closed, the engine would start the compression stroke.
Even though you weren't at TDC, you were well into the compression stroke (both exhaust and intake valves fully closed), and should be able to set the valves with no issues.
Important EDIT:
Recheck your valves at true TDC; at 1/4 turn after BDC, the exhaust lobe MAY be at/on the auto-compression release, which will throw off the exhaust valve measurement.

 

The simplest, most surefire method to adjust the valves and NOT do it on the wrong cycle:
Pick a cylinder. Remove the adjustment access covers. Rotate the crank in the normal direction of rotation and watch what the valves are doing; watch for the exhaust valves to open and then close, then the intake valves will open and then close. Once the intake valves have closed, start watching the flywheel for the TF or TR (depending on what cylinder you are doing) mark to come around to the viewing port (about 1/2 turn of the crank). Adjust all the valves on that cylinder.
Now do the same process for the other cylinder.
Done.

 

It don't get any easier than how NovaKaw650 posted it .

 

The only other thing I might add is that the engine has to be dead cold. A good rule is it should not have run in at least 6 hours. Don't do one cylinder then run it...even for a second, then do the other.

 

I will check the fronts again this Friday.

And the motor was stone cold, had not been run in days.

If its not the valves, what else could it be, fuel related, CDI related, battery is less than a year old and is on a tender.

 

If you used 1/4 turn on both cylinders, then check them both.

 

Only 1/4 on the front, 1/4 on the rear was close to the TR so I used that.

 

I have a new channel and moved the video. My old channel will be deleted in the next couple months. Here's the new channel and video

Kawasaki V Twin ATV Valve Adjust wmv: http://youtu.be/CS9ciSKb-4I

 

Long time no see, Camo!
Link didn't work, but copy and paste did.

 

Valves are perfect, re-did all of them to make sure.

Still coughs and spit, seems wants to fire...finally does.

I think its fuel related, or maybe not enough back pressure now with the exhaust (kinda started doing this after the exhaust went on)?

Any ideas?

 

While I don't have time to deal with the other questions, exhaust back pressure has nothing to do with starting.

 

I was having a hard time starting and valve lash was what I thought to be ok. Turned out that my intake valves were worn out and had sunk past the valve seats and into the heads. Maybe time for head work.

 

Man just do the basics..compression test, leak-down test, spark and timing, fuel and air & carb boot inspection.