For the screw hatch, probably you will find something that fits here: http://www.sealectdesigns.com/products/deck_plates_hatches
For the larger opening there are plenty of DIY options. All involve a soft closed-cell foam something for sealing and a stiffer something for the hatch.
Paddler's Truck Rack
Sport Cases (Electronics)
Kayak & Canoe Outriggers
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