This is not abnormal. As a matter of fact, I have to cut every intake on almost every build by the thickness of a gasket. It's also not abnormal for one side to sit differently than the other side. If you have a borescope, you can check port alignment with the intake sitting on the heads with no gaskets. If the roofs of the ports line up, then I'd cut the intake flanges and bolt it on.
Hmmmmm....seems pretty strange. Assuming the valve cover rails on TF heads are the same height as OE (are they?), then how did that OE intake ever fit anything? As a first order of business, I think I'd be checking how the mounting bolt holes line up with gasket installed and then the port roofs second. If the intake lands on the sides of the bolts before the intake seats...... that's no-good.
If the bolt holes and ports line up, you cut the VC rail height on the intake. If they don't, you cut the face of the intake until the holes line up, preferably with the intake holes sitting slightly high so they center when you pull the lid down. -Just me.
I suppose, if everything lined up great except the valve cover rail height, and you didn't want to cut your OE intake, and the valve cover rail height difference was relatively modest, you could just make up the height difference with a partial gasket under the full gasket. -Bring your gasket adhesive!
On other engines, milling a step in the intake face to accomodate the valve cover overlap is pretty common but FE intakes are unique with the shared valve cover rail feature.
Best,
Kelly