Yo:
The first time I adjusted the valves I saw the intake was tight (but the exhaust was not), too. The service man at the dealer told me this is typical. Your intake tappet never reached the same level for 2 reasons: first, the two are offset; second, the intake may simply be tight (i.e., needing adjustment). The valve guides/seals are made of very soft metal and deform over time. Also, if you study the valve train, you will see that as this happens the tappets get tight, not loose.
The easiest way to see what is happening is to take the right-side engine cover off. That way you can actually watch the cams and tappets. Do it the first time; from then on you probably won't have to bother.
1.) Take the right cover off.
2.) Take the plug out. That way you can turn the motor easily.
3.) Put the bike into 5th. gear.
4.) Use a wooden dowel, and stick it into the plug hole until it touches the top of the piston. I have read some guys post that they use a long screwdriver - I don't advise that.
5.) Stand on the left (gearshift) side, and gently bump the engine in the running direction with the rear wheel, all the while fiddling the wooden dowel with your free hand so that it does not get bound in the hole and break. With a little bit of practice, you can feel when the piston is coming up to, crossing, and going down from, TDC. Go right to TDC and stop. Quite a bit of slop either side of TDC is okay - when you look at the cams you will see why.
6.) Go to the right side, look to see if the cams are on the base circles of their respective cams. If not, rotate the engine until they are on the base circles. If you took the dowel out of the engine, you can do this from the right side as you stand there looking at them.
7.) Adjust the tappets.
8.) Put everything back together.
The first time you do this, you will have to replace the right-side engine cover gasket. This will be the last time you ever have to replace it if you use a single-edge razor blade to scrape the metal surfaces. Scraping them like this preps them for the new gasket, and leaves gasket material in the tiny holes in the surfaces so that the new gasket material doesn't meld into them. (Do this every time for every gasket, and you may never have to buy a new gasket again. I found this to work even with the head gasket.)
There is nothing magic about adjusting the tappets. All that is necessary is that the tappets are on the base circles of their respective cams. This is the point at which the valves are "relaxed," so that adjusting really is adjustment. With the right-side engine cover off you can actually see why and what is going on.
Good luck.
Paul