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At some point you may need to step away from the conversion project and look for something more suitable, as it strikes me that you're getting deep into SOW'S EAR --> SILK PURSE territory. Been there and have the T-shirt collection! ;-)
Getting in and out of the yak with Keel #2 might be next to impossible unless at the dock, and I can see how launching in shallow water could also be a challenge. Do you have experience with other kayaks? Some of the tracking issues might be paddling style more than hull design, just sayin'... Have you tried a longer double paddle, or one that can be offset 90 degrees?
If you must modify the boat I'd be tempted to go for the tried and true option of a leeboard. Easy to rig and remove, and can be pulled up to allow entry & exit in shallows. Lots of ways to attach leeboards, check out the Interwebs images for sailing rigs for yaks and canoes.