Bought 2007 gs500f recently that ran on only one cylinder due to bent valve. After replacing cylinder head, and doing timing it would crank but not start, even with starter fluid. Checked for air, vacuum, spark and fuel. I checked the timing over and over with no clue what could be wrong. This evening I thought to stick a screwdriver gently down the spark plug hole and found that the RT mark that should place the left piston at TDC does not line up, but instead TDC on the piston is coinciding with the . between the R and T on the pickup. Did the previous owner just do some incorrect mechanical work and mess this up, or has anyone seen this before. Do you think any perm damage was done to the bike. And if I set the timing to TDC where it is at now despite the mark on crank will it run ok, or will this negatively effect the bike?

Many have advanced the ignition timing by rotating the plate that holds the pick-up coil/coils CCW so the rotor triggers the spark sooner.  If it was done by altering the plate the 2 holes that hold it to the housing would be slotted.  The timing on the later bikes is not advanced as much as it was on the older models at idle for polution regs.  All have same 40* advance at higher rpm's.  All were changed to E-33 (CA) specs starting in 01-02.

PS:  Also there are/were offset rotors on the market for the GS to advance timing that might relocate TDC mark the same way.   

If the right cylinder is supposed to be at TDC when the pickup is aligned to the RT mark, but instead the left cylinder is at TDC when the pickup is aligned to the .  between the R and the T. How should I time it. Despite the marks on the pickup, Do I need to just set the right cylinder at TDC and put the cams in like normal from there? Or what should I do to time this correctly?

I pulled my head 10 years ago to replace a broken exhaust valve caused by a sticking bucket and put it on the mark shown in this pic which is same as shown in the diagram above for camshaft reassembly with 2 coil pickup and it fired right up when I was done.



Now on your engine (if it's not already done) I'd put it on the RT mark as shown in diagram above for single coil pickup and set chain/cam for arrow 1 and then move it to point between R and T where you found TDC to be and see which one puts arrow 1 closest to the cyl head finish, we don't know if your timing has been modified as discused above.  Don't put right cylinder up and time from there, use the signal generator marks.

After you have cams and tensioner assembled turn the engine over slowly and carefully a turn or two with wrench on big hex on rotor to make sure there is no interference.  A compression check would confirm proper valve timing and if it still won't start there must be another problem.

So you are saying try timing the cams with the pick up on the RT | mark, how it is displayed in the diagram, and then also try placing the cams with the left cylinder at TDC and see which configuration places the #1 on the exhaust cam closest to being in line or flush with the cylinder head? I have tried timing it several times the way the diagram shows turned by hand and also tried to start. Everything seemed to move freely and easily just wouldn't fire, obviously due to valve timing. The last time I just found TDC on the left #1 cylinder and placed the cams from there, which is when the pickup is one the . between the R and T. This placed the number #1 line on exhaust cam very close to flush with the cylinder head, also turning by hand, got small amount of resistance, but still turned and nothing seemed to be hitting each other. I broke my worn out main fuel line and am waiting for another so I have not tried starting. If everything seems to be moving freely do you think I should try to start it like this? Or should I try and do compression test first?

I'd do a compression test while waiting for the fuel line.

Argh....................

I read up a technique for this procedure online.

Not knowing there was a difference between the old vs new, I used the 89-02 image to time my 2007 bike. 

And of course the bike never cranked up.

So I just have to redo it with the crank lined up like in the second image and it will work....

I wish I had seen this sooner.