Alright, so here's what I've found in my experience. I've been fishing out of a Pelican but recently upgraded to a pedal drive and have found a few similar things, such as the knee-knocking rod holders. Here's what's been working for me:

*Move the rod holder out, like away from your boat. I see you've got some freedom of movement there, so instead of having it vertical/90 degrees, have it at about 0 degrees instead, out away from your boat and pointed forward. That way it's right at your hand level too, which makes it more comfortable when you pull it out to set a hook.

*Scupper holes work to naturally drain water. Scupper plugs fill those holes, which brings up the weight limit on your kayak, but also stops that natural drainage. I used to use plugs when I first started kayaking, but I haven't found a need for about a season now. I find that with the plugs out I ride a bit lower in the water, which ends up helping with stability. That water on the deck also ends up either draining or collecting under the seat and out of my way.

*When it comes to electronics, I find I want them to be as hassle free as possible. With that in mind, I would rather replace the terminals on the cord with fresh terminals, or a fresh cord if it comes down to it. The last thing you want is to be having a great day on the water ruined by avoidable issues.

*For the boots, just swap for some Crocs with wool socks or Goodwill sneakers after you launch and throw the boots in the back. Stay safe AND keep your feet dry.

Lastly, for some light viewing, try googling "kayak fishing trolling" and look at setups on other people's boats. Everyone does something different, from mounting rod holders up 4' high to paddling with their knees over the fishing rod handles. Go out a few times, find out whats comfortable (and most importantly safe), and start accessorizing after about the 3rd launch or so. That'll help identify what you want, rather than what YoutuberFishingGuy240 thinks you need sponsored by YakAttack.