I would inspect the soft-top compartment seals (will you have the soft-top lid painted?), as any water entering here could collect in the compartment and/or leak into the areas behind the seats and doors. The window seals are also an area that leads to water collecting on the floors. The trunk seal is an easy one, and removing it before the paint-job will make it easier to install a new one afterwards.
WAQAS in Austin, Texas