jsdeprey, Also check to make sure you have the inline (for lack of a better description right now) Circut breaker. It should be mounted on the firewall in the engine compartment, just above the brake booster/master cylinder. It will be a small rectangle relay type bolted to the firewall with two posts on it, and a wire on each post. This is for the power top and power windows.
(I know it well for the 67/68's just not sure if they changed it at all for 69?) So maybe check the manuals too, just to cross reference?