Freya Hoffmeister also had a problem with her Epic due to quality of the hull if I remember correctly. She had a specially built boat also for the journey. I would be worried about a production boat in that case. If I had to change that much on a 2 year old kayak I would not be happy. That is just my personal opinion.
Doing the things below seems more like a redesign for design problems than personalizing the kayak. Your kayak is not a race boat as far as I know. I can see a super light weigh race boat not taking abuse because it is purpose built. My friend has a new Epic surfski I hope to paddle this winter.
Just my opinion.
"I've made some modifications: reworked the straps that hold the hatches closed (these have been replaced by cams on the newer boats); replaced the bungees with stronger, thicker ones; replaced the Spectra rudder cords with stainless; reworked the architecture of the foot pedals. I've also filled the articulated-stern rudder with spray-in minicell foam to eliminate a leaking problem thru the bolt-hole that holds the rudder to the boat, and have twice epoxied the rail that the seat slides on back onto the hull interior."
'08 CD Solstice GT
'03 CD Extreme
'10 Ocean Trident Prowler
'10 Hobie Quest.
'11 Eddyline Journey