I DID ALL THAT! So when I go back to the 'Sealed Hatch' to get into the Ebon Hawk, it says that the 'Door has been magnetically sealed and can be only opened at the bridge' or something to that nature.
Be sure to save your game before you exit to your ship, and be sure that your main character is outfitted for a fight, especially if you’re of a Dark Side bent. You’ll have to fight your way back to your ship, of course, including through the Twin Suns, but you should be able to make it without any problems. This will drop the ship’s cloaking device, and also shut down the sealed hatch that prevents you from getting back to the Ebon Hawk. What you really need to do, though, is access the Bridge Command Console, use the Power Distribution system to shift all systems to secondary power, then Shutdown the power. You can use it to shut down any remaining droids on the ship (although you’ve likely killed them all). It requires a high Security to access, though, so use T3 to bust it open. After you make it past the Interior Defense and onto the Bridge of the ship, you’ll have to open the Plasteel Cylinder in one corner to gain the final access codes.