One thing I noticed is now I hear the valves ticking. I know I heard them when I first bought the bike, but I never noticed they went away until I swapped the shims and the ticking returned. I'm assuming that's a good thing, right?
No, I don't think you should hear anything, not with the very small clearances that these valves run. I think you're going to have to start over again. There is really only one, or possibly two shims that's going to be right for each valve, not a selection of shims. That is because the entire allowable gap range is the difference from one shim to the next.
I'm going to talk in inches here, and round the numbers off to an understandable set of figures.
The intake valve clearance has to be between 4 and 6 thousandths of an inch, or .004" to .006".
The exhaust valves run at between 8 and 10 thousandths (.008" to .010").
The shims are roughly 2 thousandths (.002") from one to the next.
Lets say you measured the clearance on an exhaust valve, and got a reading of 11 thousandths (.011"). You could remove that shim, determine its thickness, and select the next thicker shim. After installing that shim, your clearance should measure 9 thousandths, or .009". This is right between the allowable .008" to .010".
You can't go one more size thicker because then your clearance would only be .007", too tight for this valve.
The best advice is probably if you're close to, or at the upper limit, to leave that valve alone. Changing the shim can put you really close to too tight.
If your clearance is tight, at or below the lower limit, then install the next thinner shim and recheck.
As far as lining up timing marks, lets try something less confusing. With the valve cover removed and the timing inspection plate and the spark plugs removed, turn the engine counter-clockwise, and watch the valves actuate. If you're doing the front cylinder, watch as the exhaust valves (front valves) are pushed open, then close again as the intake valves start to open. Keep turning the engine over until the intake valves close, and then continue to turn the engine another 180 degrees. This will put that piston at the top of its compression stroke, or slightly past, and both the intake and exhaust valves can be adjusted at this point.
Repeat for the rear cylinder keeping in mind that those exhaust valves are at the rear of the cylinder head this time.