Can't setup shifting on Shimano Nexus 7 after unscrewing wheel I had to unscrew rear wheel to replace inner tube. I haven't fully detached it, just to the moment I was able to replace tube. After reattaching wheel I can't setup gears shifting (that's my first time actually). As I read in different guides I need to rotate adjusting barrel until markers are matched on speed 4, but using this barrel I'm able to match it only near speed 2. 

What else should I adjust? Or have I done something wrong (maybe reattaching wheel)?
4th gear and lining up the dots is only necessary when you are setting the cable length (during installation). You do not need to deal with that if all you did was remove the wheel. Shift so that you have enough cable to slide into the proper groove and hook the cable fixing bolt to the shifting pulley mechanism. I sometimes use one thumb to rotate the attachment point on the pulley forward to make it easier to slide the cable into place. See page 26 here https://si.shimano.com/pdfs/dm/DM-SG0003-00-ENG.pdf

Your wheel appears to be in the correct location based on the bite marks from the now-removed axle nut

Check all points on the cable to make sure a ferrule is hanging you up.