When I was first learning how to slalom and started trying the course I had some of the same issues with crossing the wake.   I found a way that helped me build confidence in my wake crossings that allowed me to progress.  I would start by moving out just to the spray line that is outside of the wake.  I would then start there and cross the wakes focusing on keeping the ski on edge.  I would progressively get more agressive with my pull across the wakes.  Next I started moving out wider trying to focus on keeping the ski on edge through the wakes.  This helped me build confidence in my wake crossings while free skiing.

Lately, I had been having trouble while skiing the course with hitting the wake real hard and getting air.  Some one told me to pull longer.  So I started focusing on pulling past the second wake and all of a sudden I wasn't bouncing off the wake any more.  Apparently I was flattening the ski too early and that flat ski was hitting the wake causing me to launch.  Plus I got a lot more width in the course and it made the pass I was working on much easier.

Your probably sore because you were using different muscle groups by keeping your knees together.

If thinking about keeping your knees right up against together works for you (this does for me then stick with it. (I've just got to remember to do it ALL of the time:)).  Regarding the straight legs thing, rather than ski with straight legs, think of your legs as being like the shock absorbers on car so you ride over the wakes rather then trying to plough through it. 'SOFT KNEES' (I've just got to remember to do it ALL of the time ).

The link is from Seth Stisher website and is of him skiing at his ski school H2Oz in Charleston. By all means watch all the videos, but first scroll to the bottom of the page and watch the last four videos, but particularly the second to last.  These are great examples of the tips you have been given, being put in practice by a top coach:

http://www.waterskitrainer.com/spip.php?page=video