Let me have a stab at explaining (4):
See the picture below:
There are two cables going from the gear lever to the gear box. One cable transmits the left/right motion of the lever to the gearbox and the other transmits the front/back motion.
By misalignment it is understood that the setting of these cables is incorrect. So lets say that when the driver moves the gear lever to the left and forward (engaging first gear), the cables do not properly move the forks within the gearbox left or right or front or back to the correct amount. Thus the driver may feel difficulty in finding the gear he/she is looking for. I hope the above explanation is adequate. If this is the the problem, correction is very easy. Just slack off the check nuts adjust the length of the outer wire and tighten check nut. Much like adjusting a motorcycle clutch cable. If there is no adjustment and the cable has stretched, then cable will need replacement.
Oh I forgot to mention that at the base of the gear lever there should be nylon bushes (items 10, 11 maybe also 7 in the picture below). If these bushes are worn, there will be excessive play in the gear lever and the net result will be difficulty in engaging gears.