I personally have not messed with a Jon-boat.
However - my Uncle, who is a retired Tool & Die guy (VERY handy / mechanically apt) modded his small 14' Alumacraft and made it MUCH nicer by incorporating the following mods:
(you could probably do similar to your boat)
MOVE GAS TANK TO FRONT: (Keeps bow down when starting out with one person at rear)
He used some durable tubing with barb fittings to move the fuel tank to beneath a plywood platform (coated in outdoor-rated vinyl) that he latched-down at the front "V-seat" to the second short seat with a stainless piano hinge and a few lock hasps to secure it down.
Then he fished the tubing through the hollow chine on the outside - where the sides meet the bottom on one side. He bored and filed an oval hole near the transom end, and another in the space where the drop-tank goes. (the Oval holes let the round gas line go-in and exit at an angle - you want to avoid sharp "kinks") Once the tubing was in, he used some grommets to prevent chafing the tubing and sealed the thru-hulls with silicone.
RE-LOCATE BATTERIES
He put-in trays with straps to allow the batteries to be tied-down. Be sure to use UV-Resistant insulated HEAVY-gauge cable [Mil-Spec wiring if you can get it - Mil-Spec jacketing does not break-down in UV light when exposed to the elements / gas / whatever...] Lace the wiring down with tie-wrap stick-on pads and be sure to rough-up and clean the surface before sticking the pads down
(he got some small connectors like what are used on Electric Forklift Batteries that he attached to each battery, to the internal wire harness, and to his charger - makes for eazy plug-in charging / swapping)
OAR-LOCK ADAPTERS THAT MAKE THE OARS ACT LIKE SIDE-RAILS:
When running - he keeps the oars socketed-in to the Aft set of Oar Locks. On the Fore set of Oar Locks - he made some Neoprene "C-Hooks" with a tab at the bottom and the opening facing Inboard. The fore end of the oars get snugged into these - it gets them off of the seats providing more inside width.
In addition to keeping the bow from coming-up too high when starting out - it also REALLY reduces the "pile of assorted crap" that you have to trip-over when operating the boat from the transom-end. It makes it feel MUCH "BIGGER" than the usual 14-footer and allows him to run things when he is by himself. (he also has a set of Anchor-mate hand-cranks at midships with custom-made pulleys that keep the Anchor Lines neat / out-of-the-way) In his case, it give him enough room to be able to keep a tackle box and other gear nearby without things becoming way too cluttered at the operator position.
Hope this provides a little inspiration for your swamp-machine (is yours for fishing the THICK stuff or more for chasing quackers?)