Yeah, as soon as you figure out how to get to the last palace (using random encounters to your advantage), you get to play through the palace as many times as you need to. Then, after you beat thunderbird, he stays beaten... and Shadow Link has to be the most anticlimatic boss fight I've ever seen. Kneel down in the left corner of the screen and keep swinging... he'll just keep running into your sword. When he does the down thrust you can either try to avoid it, or just take the damage and heal, he'll die VERY quickly and without much thought.
Actually, the hardest part of the final dungeon is finding your way through it without getting stuck in the looping sections