If you feel the first few weeks are a waste of your time, then jump to where you feel it would be challenging.
For another program, go to specialtactics.com (AFSOC PJ site). Go through the workouts section, and print out 'The Workout' by (I think) Bull something or other. I used it to prep for SWCC training, it combines lifting, running, swimming, rucking, and calisthenics into an 8 week program. Got me in awesome shape, then I went to SERE en route and detrained like a mofo. PM me your NIPR email, and I will send you a copy of the Horsemen Program, it was put together by a couple guys from SEAL Team 4 (I think), basically a well organized mash up of crossfit, gym jones, mountain athlete, and some other stuff. Oddly though, swimming is not included in that one, so you would have to adjust it to fit.