Another one of those valve cover questions

Couple items...I swapped like 4 sets of VCs on mine....height wise it might be close if your running an SN95 elbow for the GT40...a fox set-up should be fine as those are around VCs should be at or a tad under 3.5" high...
I ran some Summit chromes that were 3.5" tall, Explorer intake, with no intake spacer, and had to dimple for the IAC as it hit just a tad...cast ones like those wont dimple....I run no EGR/smog so can't help there...

PCV nipple on the drivers side may have to shortened to as odds are it will hit..

You'll have to swap over to a breather cap with a vent tube on it to feed that oil line vent tube the stock one has...with your GT40 run a breather on the pass side and youll be fine...

See the FRPP breather with the line on it....this will work for you....just feed that line to your CAI...