In the main menu, on the right-hand side (below Character Configuration and System Configuration), there's a HUD layout section.
If you select that, you get a drop-down menu listing most of the HUD elements (except for the chat-box, for some reason), with outline boxes of where they all are (since some may not be on-screen at the time). Selecting a HUD element from the drop-down lets you move or re-size it. (Moving is with one of the analog buttons, but I can't remember off-hand whether it's the left or right one. One of them moves the selected element and the other moves the little window with the drop-down list.) I think it's triangle to change sizes (which alternates between 5 different available sizes).

Windows (like character window, crafting window, inventory, etc) work a bit differently. Those don't appear in the HUD layout interface, but you can drag them to where you want. If using a controller, switch it to mouse-mode with L1+R3, open the window you're interested in, and drag it to where you want. (In mouse-mode, R2 and L2 act as right and left mouse buttons.) The only awkward part is that a lot of such windows reassign the L1 button for changing tabs, so you can't turn mouse-mode on or off while the window is active. Set mouse-mode in advance before opening the window to avoid that problem. Oh, and it's windows like these where the L3 or R3 (I can't remember which one either) work to re-size them.

Things like the mini-map would be done through the HUD Layout section.