I'm running a stock 1988 aluminum intake with Pacesetter headers. The way that setup worked out I ended up having to make some "half-washers". They weren't exactly half a washer, more like 2/3. This allowed me to make up the approximately 1/16 inch difference between the header flange thickness and the manifold flange thickness.
Basically, I took a die grinder with a cutoff wheel mounted and cut the washer so I barely intersected the hole. It was a little bit of a trick clocking the washers during the install, but it's not like I take the manifold off every day so I just dealt with it.
If you look carefully, on the back side of the front header tube you can see the extra washer under the bolt. You will also notice that the intake flange is a little thicker than the header flange. I've been driving it like this for a few months now and really seems to be holding up so I think it is a permanent solution.
If you want a closer look, PM me and I can email you the full size shot tomorrow. I'm just about ready to leave work but I'll throw it on the USB drive tonight for you anyway.