OK, going through here I found a few key comments and suggestions. Early on there was mention of a crate, that crate contained 3 water bottles, 2 full, one empty and used as a urinal. Some folks forget the convenience of keeping a pee jug in the boat. My personal recommendation is a 32 oz Gatorade bottle. The large opening and higher capacity makes things just a wee bit easier. Continuing on to the crate, there are hundreds of kayak crate building videos on YouTube, watch some for ideas. This is one stupid easy project that you'll use forever. Think when you build it, though. I put 4 rodholders on mine, made from 1 1/2" PVC. I built it at work and brought a rod to test it out. The first trip out, I realized that my favorite short handled casting rod, equipped with a pistol grip, doesn't fit in a 1 1/2" pipe, and I had to leave it in the truck and stick to the spinning gear. Don't do that.
As for the PFD's, find one that's comfortable. If you're looking at a chain, get a kayak down similar to yours, grab a rod, grab a paddle, and try the life jacket on in the store, sitting in the boat, paddling and casting. Also, don't be scared to pick up a type IV PFD as well. This may not be legal as your only PFD in your state, nor is it really a good idea to have as your only PFD, but they do make a good seat cushion that can also be used to save a life. You can find them as cheap as $10.
Anchor trolleys can be made out of paracord, a key ring, and a couple of U bolts or plastic eyes. If you plan to anchor the 'yak and fish from it, this is a great way to spend $5, and it works with a stake out pole as well.
Waterproof cell phone - I have been an avid user of milspec phones since the days of NEXTEL. Kyocera makes some very nice units. I've had several TORQUE models and currently have a Dura Force XT. Totally worth a look if you're upgrading and do anything that might break a phone. Something that has been missed, however, is that waterproof phones do not float, and neither do Lifeproof cases or any Otter Box. Your phone will float just in a baggie, and your day on the pond will be much better if you leave the phone in the truck.
Continuing with the waterproof phone, if you're looking for electronics, there are a lot of lower cost options out there that work with your phone. There's iBobber, Deeper, and a half a dozen other ones. Worth a look. Most will work with your old phone so you re less likely to cry when you dump it. I use my Deeper with an old Kyocera Torque. The old phone also has about 30 Grateful Dead shows recorded on the SD card and works great with a waterproof bluetooth speaker.
Do you smoke? Find a waterproof cigarette case. they'll hold a pack of smokes, a lighter, ID, credit card, and some cash, and they float. Seeing as marijuana is legal in some states now, I'll add that a wooden dugout and one hitter will also float, however I'll point out that boating under the influence is illegal and ill advised.
As for the other things that you might need, check your local laws before you go out. You may want a battery operated stern light and an extra rod holder on your crate to put it in (or a go pro on a stick). Your state may also require a bow light. A whistle or an air horn is a good idea and a legal requirement in some states (often it must be audible for 1/2 mile). Launch permits also vary from state to state.
What are you driving? Trailer, roof rack, back of the truck? A proper rack can protect your yak and your car. Pool noodles can also be the answer.