valve not seating propelly.

hello every one
ok so this is a new problem for my 1981 kz1300. i have been working on the bike for three years, i do a lot of things to make it perfect and unable to do so. but there was my planning for this summer.
1- disassemble the carb clean it well with "Scotch Cleaning tool's" .. it's done.
2- valve clearance and adjust if necessary.
3- heat it up and synchronize it.
4-color set and then, if it's not right, I'll ask for help, but there is a problem with # 2.

I did not check the compression before adjusting the valve. I took it last summer and here are my results.
cyl # 1 115 psi
cyl # 2 110 psi
cyl # 3 90 psi *****
cyl # 4 120 psi
cyl # 5 110 psi
cyl # 6 120 psi
this valve job was my first and everything is going well. I need to adjust my inlet and outlet # 6, my outlet # 2, my inlet and my outlet # 4. So I had 5 shims to change. Yes I made a mystake I changed the n ° 2 shim which was too thin and I put a thinner one.
I buy a brand new compression kit from mytivac, it's a good one but now the compression is.
# 1- 140 psi
# 2- 55 psi ****
# 3- 90 psi
# 4- 145 psi
# 5- 130 psi
# 6- 110 psi
I removed my valve cover again and realized my mistake on # 2, so put the right shim this time, took the compression still at 55psi.
I can see through the candle hole a black deposit and a little white and this particular valve. I did the cylinder leak test and it clearly showed the problem was the # 2 outlet valve, which was not seated properly. the bike has not started since last summer 7 months.

do I start the bike and heat it up to check if the carbon and white deposit has burned off and take my compression when the engine is hot or just pull my head off to see what's going on in there, could i have done something wrong and am wondering if the head gasket is not damaged between cyl#2 and cyl#3 .

What is your suggestion. thank you for your time and knowledge. Simon Ldemon??

Compression "checks" are a great quick tool just to see if things are ok but as far as a diagnostic tool, useless. The ONLY information that I use a compression test for is to indicate the health of the timing chain. As the timing chain stretches, the intake and exhaust valves retard in timing and the more retarded the intake valves, the less compression is created.
The only true way to determine "what's going on" is to do a leak down check. While doing a leak down check you have all the sparkplugs out, the rad cap off and the oil filler cap off. Air is applied to the leak down tester which is screwed in to one of the spark plug holes and air is applied to that cylinder at 100 psi. The reading is taken from the leak down gauge as a percentage. 5%  is a good tight motor, 10% is a ok and not needing any attention yet. 15% leak down and you should be considering doing some work. 20% would be my maximum acceptance.
During the leak down test you can listen for the "leak" at the carbs indicating a leaking intake valve, Listen at the exhaust  for a leak from the exhaust valve. Listen for leaking at the adjacent spark plug holes indicating a leaking head gasket. Look for bubbles at the rad filler cap indicating a bad head gasket. Air leakage at the oil filler cap would indicate piston rings.
Normally, i like to take 2 readings. One at bottom dead center (which is the safest) because when you apply 100 psi to a cylinder, it will drive the piston down to bottom dead center. I also like to take a second reading at 20 degrees before top dead center and hold the crank shaft at that point from rotating. The reason I choose 20 degrees before top dead center is that cylinder wear at that point is in the area where most wear is and I want to know how bad the cylinder wear is. At 20 degrees before top dead center, the crank wants to  drive counterclockwise and by putting a wrench on the crank and holding it clockwise will be reasonably safe.
Based on the leak down percentage, you may have one or more issues to repair like intake and valve seats, or piston rings if there's  air leakage at the oil filler cap. But at least you'll know when you teardown the engine exactly where to focus your attention. All the guess work has been done.

The basic design of a leak down tester is air is supplied at the inlet of the tool and regulated to 100 psi indicated on the inlet gauge. That 100 psi is forced through a .040" orifice and delivered to the spark plug hole of the cylinder being tested. If the "leak " in the cylinder is less than the amount of air going through the .040" orifice, then the pressure will be indicated at 0% leak down. Any leak greater than what could pass through that .040" orifice will cause the indicated leak down to show as a  percentage of leak down.
So if lets say your engine is capable of 130 psi compression and you had an indicated leak down of 10%.  10% of 130 psi would be 13 psi, so the compression of a cylinder at 10% leak down would be 117 psi. The leak down tester only indicates a percentage of leak down but you can see the relationship going on here.
Based on your reading of 90 psi on #3, I would need to understand that. It's consistent with a previous compression test and as previously stated, 20% leak down would be my teardown point. 20% of 130 = 26psi. 130-26=103 psi and you indicate 90 psi on compression test. A leak down test will tell you definitively what the problem is.
Hope this helps

Thanks for that information kawboy. 
I know 90 psi is not good for compression and the cylinder have way too more different betweens each other. Over the last three years a probably did 10 compression test and it's 90 psi every single time. I will do a more accurate leak down test to know from where are the leak. 
I got fear that my head gasket is deteriorated between cylinder #2 and #3.
Last summer I give it couples of real ride, savage, maybe he didn't like it.
Thanks for the reply good work.