I did this upgrade 2 years ago and used the instructions put together by Schoir and Boxtaboy (and others?). The 2004 top bolted into my 2002 very easily, but the latch just barely touched the plastic wind blocker upon open/close. I checked with Boxtaboy and he said there is some adjustment in the mounting, although it may not seem like it. I loosened the 3 mounting bolts on each side and had someone apply pressure on the frame toward the back of the car as I re-tightened the bolts and everything worked great. I did sometimes have to pull the top forward a little when I latched it (which I didn't have to do with my original top) but after a few months on the car everything must have 'stretched' into place and had worked perfectly since then.
Your issue must have to do with the same mounting adjustment, and minor differences from the donor car to yours.
Did you have the header latched as you tightened the mounting bolts? I think I had the top in the service position when I tightened the bolts, which may allow more adjustment.
Check out the links below, if you haven't seen them already. You could also PM boxtaboy or schoir as they were the experts back a few years. I think they are still active.
Good luck! It is a great upgrade that you will love when it is done.
https://sites.google.com/site/mikefocke2/installinga%2703-%2704glasstopandframeona%2797
http://986forum.com/forums/general-discussions/20414-2003-oem-glass-convertible-top-installed-01-boxster.html