Actually, I'd imagine that a problem with the cam caps would not affect the clearances like that -- basically, in measuring position, the cam lobe is not pushing down against the valve spring. The positions of nearby valves could affect this, but I'd have to open up my engine and sit down with a beer and stare at it a while to ponder this.
Also, just to be contrary, I've never found a difference in valve clearances between following the Suzuki procedure exactly and simply rotating the engine until the cam lobe for the valve I want to check is in the right position. Some folks have. FWIW, YMMV, etc. I expect violent disagreements to erupt over this heresy...
To be fair, I haven't repeated this experiment (Suzuki Way vs. My Way) on every engine I've encountered, but usually I just set the #1 exhaust lobe to point straight away from the cylinder head, then do the same to #2, #3, #4, etc. and then do the intakes in the same order. It's easier in my mind to simply rotate the engine more times than to risk getting disorganized.
ANYWAY... back to the OP's problem:
It really sounds like either the engine has had work done in the past, and whoever was in there last just did the best they could with the commonly available shims. If the valve seats have been re-cut, many builders will grind the ends of the valve stems to match, and they may have gone a wee bit overboard. Not a problem if you can find shims large enough, and it sounds like you can. (Can you post which shims are in there now?)
The other possibility is that carbon buildup on the valves is propping them open. This is pretty uncommon, but I guess it's a possibility. How has the bike been running? Are the plugs black and gross, or are things pretty good mixture-wise?
And, um, the engine was room temperature (not run for at least 12 hours) when you measured the clearances, right?
So here's what I'd do, assuming it's running well:
Button it up, ride the living snot out of it for another 500 - 1,000 miles, and re-check the valves. If it was carbon buildup, the carbon will get hammered out of the way and you'll get the "true" clearances.
If it's just big clearances (they're all about the same as previously), drop in a larger shim on the #2 intake and don't worry about the others.
There's nothing at all wrong with using inch feeler gauges. I used them for years until I finally found a set of metrics. It's just a little easier mentally to work in mm. I dunno about you, but my mind needs all the help it can get.
Also, the metric set has more feelers in this size range -- mine has one for every .01mm from .03 to .15. So there.
Also, just to be contrary, I've never found a difference in valve clearances between following the Suzuki procedure exactly and simply rotating the engine until the cam lobe for the valve I want to check is in the right position. Some folks have. FWIW, YMMV, etc. I expect violent disagreements to erupt over this heresy...
To be fair, I haven't repeated this experiment (Suzuki Way vs. My Way) on every engine I've encountered, but usually I just set the #1 exhaust lobe to point straight away from the cylinder head, then do the same to #2, #3, #4, etc. and then do the intakes in the same order. It's easier in my mind to simply rotate the engine more times than to risk getting disorganized.
ANYWAY... back to the OP's problem:
It really sounds like either the engine has had work done in the past, and whoever was in there last just did the best they could with the commonly available shims. If the valve seats have been re-cut, many builders will grind the ends of the valve stems to match, and they may have gone a wee bit overboard. Not a problem if you can find shims large enough, and it sounds like you can. (Can you post which shims are in there now?)
The other possibility is that carbon buildup on the valves is propping them open. This is pretty uncommon, but I guess it's a possibility. How has the bike been running? Are the plugs black and gross, or are things pretty good mixture-wise?
And, um, the engine was room temperature (not run for at least 12 hours) when you measured the clearances, right?
So here's what I'd do, assuming it's running well:
Button it up, ride the living snot out of it for another 500 - 1,000 miles, and re-check the valves. If it was carbon buildup, the carbon will get hammered out of the way and you'll get the "true" clearances.
If it's just big clearances (they're all about the same as previously), drop in a larger shim on the #2 intake and don't worry about the others.
There's nothing at all wrong with using inch feeler gauges. I used them for years until I finally found a set of metrics. It's just a little easier mentally to work in mm. I dunno about you, but my mind needs all the help it can get.