cbr600 fy valve timing

[skyline]

Hi just doing the valve timing on my cbr600 fy (dorris for those who know it on here ) and have a couple of questions.

First one is when I set the line next to the T mark ( looks like TI on the timing) to the notch on the crank case as according to the 'haynes book of lies' it says the 'in' and 'ex' marks on the camshafts should both be horrizontal to the crank case facing away from each other. how ever as shown in the first pic below the 'in' mark is futher down by a tooth or maybe 2 (by estimate, also the ex mark looks alot higher up but thats because of the angle of the camera although it is slightly higher than the crank case on eye level i just wanted to the show differences in where the marks sit to each other) so when checking the valve clearances do I want the 'in' mark to be level with the crankcase, or the TI mark exactly on the notch?

Ill point out at this point that that the bikes been used for track days and drag strips and has been on dyno runs so i dont know if the timing could of be changed intentionally or would this not class as a timing change (im not sure)

[Bendy]