It will fit the valve covers fine with no mods. The issue comes with the routing of the intake tube.
I'm running a Mustang intake manifold ('87-'93), it clears the blower box, but a 90* tube off the throttle body hit the edge of the box. Other setups (aftermarket, '94/'95, Explorer, etc., may not have this issue)
I removed the AC from my truck. replaced the heater box with a non AC version, which is the same moulding. So this whole section is now empty with no (evaporator?) inside. So I cut it off and fibreglassed it.
FWIW, a pre-'95 box will not fit, (the kind you pics of being modded for valve cover clearance) as the firewall is different. I bought one to try, that's how this was figured out.
You can see clearly here, no mods:
A friend's truck: (GT40 on RPS) Not modded, but AC not currently hooked up. (it's a short FEAD setup, (off '93 Cougar, similar to '94/'95 'Stang, Explorer) and uses the rad in stock position, leaving rome for the condensor in front of the rad)
Guess I don't have a clear shot of the modded box in photobucket, but you get the idea.