Bike drives good, I checked alignment, I think, it is very close to perfect, but rear wheel is not in the center of rear fender. Any ideas?

 

Bike drives good, I checked align. I wish mine were perfect.
You see and hear the rear tire not even with the sides of the fender here on the forum all the time. With all what you have said there is nothing probable wrong with it. What did you align? Most Harley do not align perfectly with the front wheel. The most important thing unless you start modifying spacers and shimming rear wheel drive pulley is to align the rear wheel sprocket with the front sprocket so the belt tracks true. Should rub slightly on the inboard side at the rear going forward. Do not try to align to front tire. You do that when you turn the handlebars. Put a picture up with a visible pull tape on both sides for us to see. I bet I get slammed here.

 

Everything is done! I got scared but it was not a big deal.
There are 9 points of rear fender adjustment. 2 bolts on each side + nut=8 and front bolt which I didn't touch.
fender/nut adjustment and bolt/nut adjustment.
I just didn't bother to adlust fender when I installed it after painting.

 

What bike do you have the fender alignment with? I have an 01RK with the same issue, only I read that it was poor design by HD. I really would like to fix this if I could.

 

A lot of them like that including mine...i checked 15 new bikes or so at the local dealers and about 1/2 were not centered.

 

Seen this on several bikes. Re-allign the rear fender will take care of it. If the rear tire was replaced after you noticed this, be sure the rear spacers are in the correct position. The other thing I saw was on a freinds Ultra after the deaeler had installed a new tire. Guess one of the techs (?) leaned on the fender and "tweeked" it to one side. Measure from the rear swing arm on each side of the tire. THere are specs in the repair manual for the clearance.