The front sub frame can actually be installed/bolted up slightly skewed, so it's not out of the question that it may be slightly out of alignment. But, this would mean you have to loosen up all the sub frame & core support mounts and see if it can be ever so slightly realigned with out having to re-adjust the front body panels.

Aftermarket fenders both front & rear have a wider wheel well lip, which could possibly contribute to your issue. Then a spacer as well will also shift the geometry of the wheel as it moves through the turning radius. So it may be a combination of things all adding up. So I think your on the right track in thinking about wheels & tires and possibly rotors/calipers to be able to use them with out spacers. I bet that will take care of it? But you may still want to have the alignment of the Sub frame checked out in the future...

Congrats on the new toy! It's all about the Smiles per mile!

Brett!