well that depends on what you mean by stock motor mounts. The stock B16 ones will, the stock d-series ones will not.

You will need a b-series AC mount, rear bracket mount, driver's side upper (cam) mount, and right front transmission mount. The upper transmission mount will work, and you can re-use your rubber mounting D-bracket thingy for the a/c mount and the rear mount.

:edit: here's a helpful picture stolen from H-T