I'm stuck..I'm pretty sure I've been everywhere... What do I do w/ the..

Somewhere in the east wing of the Mansion 2F is a holding device with the actual shotgun in it, take the shotgun then put the broken shotgun in it's place.

Collecting three MO-Disc's are required to free your partner at the end of the game.

Go to 'check' on the doom books, then move it to where the pages are facing you. Choose 'examine' (or something of the sort) and the book will open, one revealing the eagle emblem the other the wolf one.

I'm not sure what you mean by basement, but theres two I think you could mean:
The first one requires the helmet key. In the west wing of Mansion 2F there is a locked door. Use the helmet key to open it. Go in, and there should be a record player in the corner. Examine it and spin it by hand almost perfectly. Yawn (the giant snake) should come back, kill him and go down the hole he made attacking you. There is a tomb stone, examine it and do the little mini-game without hurting yourself. Then you will be in the basement.

OR if your talking about the underground, it's a little harder to explain. You should have found a battery along the way. In the garden, go to the inactive elevator and put the battery in. Go up it and use the crank where you used it the first time to refill the place with water. Go down the elevator you just fixed and Somewhere in that lower area will be a narrow path that was blocked by falling water. Go down the path and there should be a ladder. Go down and your in the underground.