Well I've solved my problems. To get to the area in the Ancient Tree, you need a Red Mushroom. To get that, go to the Lifeless Town during the night, use the Warp Magic Square, and go to where GariGari boy is. Snake will be there, and he sells Red Mushrooms. Go back to the Ancient Tree, and to the second room on the way to the Red Key. There will be a hole. Use the 'shroom to find Snake yet again, after solving a block puzzle to get to him. The Earth Warp Square, as I read on the Boktai equivalent of RPM, is accessible after getting 210,000+ Soll on playthrough 2+. For the room in Pirate's Island, use the Warp Magic Square and then a Red Mushroom. Discovery? GariGari guy or Snake, depending on the time. Hope that helps!