Embedded nuts seems like a lot of fiddly work. Why not burying in the epoxy a stainless strip with machine screws affixed at regular interval? Once the epoxy cures you will have a long row of screws sticking out of the hull, ready to attach your C track to it with small nuts (just wax and tape the threads to prevent epoxy from sticking on it).

The inconvenient of this method is that you cannot make the nuts flush with the hull, mmm...