Ok, I have a couple of questions and maybe you guys can point me in the right direction. I am currently in the Marine Corps and serving as an infantry Marine. I consider myself to have thorough knowledge about fitness and what it takes to be competitive. I am currently getting ready to submit a package for CCT. I went through Assessment and Selection for MARSOC last year and I was selected, but decided not to go through school due to the fact that I had to sign another 5-year contract before I went through the pipeline. This was a big risk to take, especially me having already a backup plan for leaving the military. Anyways, here it goes:
My goal right now is to be able to perform well on the PAST, since I am attempting to cross over from the Marine Corps, my performance on the PAST has to be exceptionally well in order for them to consider me, since the AF will be taking a risk on me. I can currently run 3-miles in 20:05 (want to get to sub 18:30), pull-ups: 18 (dead hang), I have to work on my pushups and sit ups, since in the Marine Corps we do crunches, which is 100 in 2 minutes. I can currently do about 60 pushups(perfect form, all the way down and up w/ arms completely locked out and breaking 90 degrees). But I can definetely complete 200 push ups in one workout.
- my current 500 meter surface swim is at 10:30(goal is sub 9:00) and I can perform a 2k fin with full gear while pushing a ruck in 55:00, this is in open water, sometimes against the current.
-Rucking: this is my strong point, I can move out at an average of 10 min and 12 min miles for 12 miles w/50-60 lb ruck plus water.

So, as you guys can see, I have what some of you might consider an imbalanced fitness level. I have been doing some research and trying out different training routines, and to be honest it has become overwhelming. I have been doing SEALFIT for a while now and noticed that my strength has improved a lot, but it lacks endurance training. I have also looked at some of the SOFWODS and some of them were too easy but then again there are a few that kicked my *****. I looked at the MC GUARD Pipeline workup and I realized that I'm at about week 5 or 6 level. I can hoenstly say that I have not tried Rescue Athlete yet.

Question: How do I put together a plan that is going to make me faster in the water and on land, short distance and long distance, also, I want my core to get stronger and want to be able to perform more pushups, situps and pullups. The Marines I work with already tell me that I'm nuts because of my PT sessions and they often see me doing 400 meter bear crawls and other SOF-like Workouts(I guess thats a good thing). Should I take something from all the resources available and put together a plan for my needs or should I stick to one that is going to provide me with the best overall results to what I'm trying to do?

PS: I'm also going to be attending Marine Corps water Survival Instructor School in August 2012, this is a 3-week long haze fest in the pool, so I know this will be a good base for the swimmming at CCT.

If you guys can give me some advice as to what I should look into and how should I approach my training routine. Thank you in advance for anyone that is willing to put some thought into my questions.

It seems as though you answered your own question. I got pretty quick in the water by mostly doing Race Pace sprints, same on land. Sprints from 50-200m depending on your ability in the water. With running, intervals 400-800m as well as fartlek training and a longer run. I actually just followed Rescue Athletes programming and got better at pretty much everything, That's just me though. Most of the programming you speak of will get you into the shape you need. Running is my weak point so I have to sub more running vs swimming. The GuardMC Trainup has some great cal variations you can do. I add his programming to Rescue Athlete and I usually good to go. I can swim, run, cals in the morning, and do the FTX at night. You already stated your weak points, so I would substitute more of what you are weak at into your programming.

You know, I was actually going over some research last night and came to the conclusion that what I'm mostly lacking is keeping track of my progress. So, therefore, I just need to be able to fit in the Workouts according to my level, and then, improve on my weak points. Meaning that I must build up on my weakness and maintain what I have gained. Seems more like a Rocket science formula than anything else. But I guess when you get to these levels of training all the small things matter. Again, thanks for your reply.