Hello, I am adjusting valves clearances on my 91 GS500e. I needed to change the shims on both exhaust valves. Prior to taking off the exhaust cam, I used a paint marker on the cam chain to make sure the chain does not get reinstalled on the wrong sprocket tooth. Thinking that I was smart, I removed the exhaust cam, changed shims, and reinstalled. The problem, the paint marks didn't line up!  I removed the cam and CCT again, cycled the engine to the RT| marking, and the chain had zero paint markings! I cycled the motor again and one paint marking lined up on the intake cam. I put it all back together and the measurements are CORRECT in the valve clearances.

My question: did I f*** up? Is the motor out of alignment if the crank sprocket isn't in the appropriate alignment? The valve clearences are correct, the RT| is lined up, but is there a chance the crank is off now? Or should everything be ok since all the measurements are correct?

Thank you!

Your timing rotor is fixed to the crank; so your engine position/ markings don't rely on the cam-chain.

Confirm that you are following the correct procedure against the manual,  re: cam-sprocket markers, 18 pins etc.

The main thing to worry about is the valve position, relative to the pistons. With that in mind, if your engine is at RT, check the clearances on the INTAKE cam
to be sure that they have remained the same, (since you have already cycled the engine.) Do not cycle the engine again until everything is confirmed.

Edit** Just looked at my Haynes manual since I'm only familiar with the newer gen engine.

for your 91': " The R.T. mark must align with the middle of the LEFT-HAND pulse generator coil"
                       "The notch in the end of each camshaft must face inwards"

Paint on the chain will NOT line up with the sprocket once you have turned the engine over (ask me how I know )
That's why you need to know where the timing marks are and how many links of chain there should be between the cams.
I haven't messed with GS timing for a while so I don't remember any specifics but if you turned the engine over and it has compression/didn't get stuck at any point you most likely put it on time or pretty close.
Spin the engine by hand (2 rotations of the crank) and if it doesn't bind try starting the thing and see what happens.