Altium Designer: Large project hanging
You could try using compile masks to import the schematic components into the PCB in chunks. This will mask out the components from the design compiler, so they won't be compiled and ERC'd, nor will they be imported into the PCB.

Then you can delete the next mask, re-compile, annotate schematics, import into PCB, and rinse and repeat. This way you don't have to delete components, just draw masks over stuff (which is just dragging rectangles) -- it's silly, but will let you chunk up the import.

What version are you using, and where are your components actually stored (Vault, SVNDbLib, etc.)? Maybe you're eating a performance hit from a network drive or something as well. Getting everything local to your machine you can may help as well.