To get both stems of a double U cordon equal in height is highly desirable. If they are unequal the longer you leave them the harder it will be to correct. If they are not too bad then you can lift the short one and lower the long one and hopefully the tree will respond appropriately.
With regard to general pruning, if the tree has reached the height you want it to be then now is the time to stop it. When stopping it obviously cut to the desired height, but you should allow it to grow a minimum of two inches this year. If the tree has not yet reached the height you want i.e. you want the it to be taller, then leave the growing tips alone for now but take off about one third of this years growth from the leaders at Christmas. This will (a) stimulate growth of next years leader (b) encourage what's left of this years leader to form spurs all down its stem which will hopefully develop in due course into fruiting spurs.
Now is the time to deal with side shoots from your vertical leaders. If the side shoot comes directly from a leader cut it back to the width of your hand. If the side shoot does not come directly from a leader (i.e. from an earlier years side shoot) cut it back to half that size.
