Your best way to make this happen is to copy the whole game system. This way you can do all your "Replace Thing ID" for all these spells but still have the original version of Pathfinder. When you start HL you would have two different Pathfinder game systems to choose. One setup for CORE and one with your houserules.
Otherwise if you "preclude" a spell and that spell is bootstrapped to make a spell-like ability or used in a gizmo for a wand you will have issues.
And no you can't REMOVE tags from a Thing. Extend can only be used to add tags.
