I would install the bulkheads before cutting the boat; if you cut first residual stresses in the boat will cause each half to deform differently and you'll never get them alined again. Mount them as a unit with spacers to leave room for the gasket, and glass them in, accessing one from the cockpit and the other from the rear hatch. This is how Nigel Dennis makes his three piece take apart. If space is an issue, you might be able to set them up with flanges instead of full bulkheads, so the bow fits into the stern, which fits into the center section.

Use stainless bolts and nut plates to rejoin the halves.