If I understand you rightly, the bolts AND the bases are epoxied to the hull--correct?
So, you can get hull & bases loose of the wooden base, correct?
If so, I's down to finding a way to change the geometry where spindles meet base..
Easy answer would be that the spindles have a base diameter that matches a Forstner bit. The Forstner would 'pilot' on the existing hole. You could tip the drill, and give you a nice counterbore in the wooden base. A brass washer cut in half could then be sued to shim the spindles to bring the hull true. If you ned to trim fore-and-aft, just cur the meedful spindle location that much deeper.
A spade drill bit, at very low speed could be used to score the counterbore's circumference. Skill with a chisel could then be applied.
Worst case, you find a hank of tubing the right outside diameter, and Dremel a bevel on the inside, leaving a sharp edge. Center that on the wood base holes, and give a smack or twain to cut down the circumference. Then, out with the chisels again.