Congrats on joinging the plastic navy! I have several friends on the JK Pro Staff and can offer one recommendation - if at all possible, keep the seats in the low position when paddling in choppy waters or heavy wind. First, it may be a tad difficult to paddle at times like that; and two, it decreases the chances of you getting tossed overboard. I had a friend who was launching at a boat ramp in some choppy water and he flipped/turtled at the ramp with his seat in the high position even after I warned him. He doesn't do that anymore
Other than that, your approach on just heading out and enjoying the experience first is a great way to start. As far as rigging, I would take a single older rod with you so you can fish some, but also take with you vaseline. What you do is place a dallop of the vaseline on the butt of the rod and while sitting in the various seating positions, move the rod around you to see what feels natural and what does not. Then, mimic stowing the rod in a rod holder by seeing how far you can reach beside and behind you. When you feel you have reached your maximum comfort zone, touch the butt of the rod to the hull. This will now mark the spot and make it easier for you when you get back home. Then you just have to decide on what rod holder to use.
I'll make a couple suggestions on this front for you that will pay off in the long run. First, draw out your plan first on paper - be precise on your measurements and know the various options out there before you go a buy something. Second, use the YakAttack GearTrac rail mounting system or Mighty Mount with Backing Plate wherever possible. Both of these moutning systems allow you to interchange rod holders, FF mounts, accessory mounts, etc by using the YakAttack Might Bolt based products like Screwballs (RAM products), VisiCarbon II Safety Flags, Scotty and RAM rod holders, etc. The beauty of the the GearTracs and Mighty Mounts is that they give you greater flexibility in positioning your rod holders for different situations.
I use my GearTracs to position my RAM Rod Tubes slightly forward and angled outwards - it serves two purposes. First, it allows me to troll with my rod tips still visible yet the rods are stowed aft of my seating postion out of the way. Second, it works as a rod storage location while I land a fish. The rod is out of the way. Third, it also makes tying leader knots, lures and baiting hooks much easier without having to deal with a rod laying in my lap.
Regarding your list of remaining items to purchase - do not purchase cheap accessories like a $50 paddle or PFD if at all possible. If you have to cut costs, do so on the PFD initially, because using a cheap heavy paddle will discourage you and increase the chances of you not enjoying your time on the water in your new Big Tuna. I recommend that people start our with a paddle similar to the price point of the Bending Branches Angler, Aqua Bound Manta Ray ($79-129 price point). As far as a PFD, USCG requirements state you must wear a Class III level PFD in most states, so make a trip to your local kayak shop and test fit your PFD while sitting in one of their Big Tunas on the floor. If the shop doesn't have any, then sit in the JK Coosa, Cuda 12 or even the Native Slayer or Ultimates. They have a similar style seat. The key with choosing a PFD is fiding one that is both comfortable and suitable for your paddling position while seated. If it's not comfortable when you paddlle, there is an increased chance that you won't wear it! Safety first!!!
Other than that, once you have your PFD, make it a point to go to the water with only your kayak, paddle, and PFD first and launch into a shallow 3-4' section where you can test out your stability comfort zone. Learn the limits of both your kayak's primary and secondary stability and your overall equilibrium and level of comfort in each seated position. Once you have that nailed down, then you can spend more time on the water focusing on the fishing and not worried about whether you are going to flip or not.
Everyone has been knocked out of a kayak or flipped it out at some point, and if they haven't they will at some point - it's not a question of whether you will ever turtle in a kayak. It's only a question of when will it happen. Most of the time, it happens when you do something beyond your normal limits and put yourself in a position where the slightest change ends up with you in the water. Like trying to unsnag a lure and leaning too far one way or the other or reaching for a fish in the thigh seat position (don't laugh - I've seen it ). It happens - just expect it and move on.
Now go out and have some fun!!