Make sure you have a solid plan to reseal everything well before making new holes. If the boat is plastic this is a tall order, if it is composite you have more options available to you. The basic composite boat can be worked on with stuff from any decent marine store like Hamilton or West Marine.
The minicell you'll be putting in to help with the rest of the fit - likely adding some to effectively lower the deck height - is not a problem. It can easily come out with solvents to dissolve the adhesive.
I understand that you love the kayak right now, but if it is truly oversized for you and you keep expanding your skills you will hit some things where the boat itself adds to your problem in learning a new skill. I am officially a small small paddler and have been there. So as much as you love the boat right now, give yourself the head room to change your mind once things warm up and you have the chance to really start getting seat time. Things that are a minor annoyance for a couple of hour jaunt can be much more so by a few hours into a full day on the water.
Full Size Sail Rig
Paddler's Truck Rack
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