A 1/2" spacer should be fine. I used the spacer that came with my Infinity Kappa 6x9 and it's about 3/8" thick. And yes, the metal door pull bracket in the back will have to be notched to clear the speaker. Before you do anything though, check the depth of your 6x9s. You have about 2-3/4" between the door frame and the window.
-Wes
98 SE Sport