For a first mod you've picked a decent one.
You'll technically need 3 controllers to do this, at least bits and pieces from 2 others including the full one the way I've done it here.
Moving the stick is pretty much how you described it, just put it wherever you want and rewire it. You'll notice in the pic here that the stick is turned from it's original position, this makes no difference at all, and is in fact how it will have to be installed because of space limitations, but just so long as it's in there 'square' all you have to do is wire it back up to the correct spots. If it's backwards you simply swap the Pole connections around. Try and keep the wires as short as possible as the sticks in the DS3 controllers are Hall Effect sensors and they can be really picky sometimes about being moved around. I used part of another controller board to mount the stick too.
You'll also have to do all sorts of alterations to the brace of the controller, so the stick has room and the shell to get it all back together. These are things I didn't get any pics of as I dislike stopping in the middle of something new to take 10 pics for the actual one that I will keep, but that mess needs to be done carefully as you have to keep the original Daughter board connection in place.
As for the D-pad, you'll need parts from one of the older PS3 controllers, before the DS3 controllers came out and the Daughter board connection was changed. You'll need the Daughter board and it's connector off of the controller board from one of those older versions of controller, then it basically gets done the same way I did the 36D controller. The connector gets wired up and run to the 5 spots on the DS3 board for the D-pad connections, COM1, DU, DD, DL and DR, then you can plug up the older Daughter board to it and there's you're new D-pad that you can place wherever. There's no need to sever the traces of the Daughter board like I did on the 36D controller, because the PS3 controller is designed to work with it.
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For a first time out this isn't what I'd really recommend trying, the PS3 controllers are a witch to work on and if something gets messed up they're even harder to repair, so be prepared to loose at least one for the cause, but take your time and work it out, it most definitely can be done.
PS3 controller info here >
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