there is for sure such a thing as too much porting
The biggest hurdle with the metal upper and lower intakes is to get a good gasket match on them and as you said some porting in the lower intake
These are not choke points for the 4.0 so there is no need to try and flow more air then the engine can possibly take in
Sven Pruett wrote the book on making power from a 4.0 ohv....literally
I have a copy, I have not seen it for many years, but it is still avail online for sale
going for $100 or more!! holy smokes
How to Build and Modify Ford 60 Degrees V-6 Engines (Motorbooks International Powerpro): Pruett, Sven: 9780879389147: Amazon.com: Books
If I have a good running 4.0 on the stand you better believe I am pulling the heads, timing cover, oil pan....I would re seal the entire engine and replace the timing set and update all of the gaskets, new head bolts as they are TTY, replace the valve seals as well
I have sealed up many 4.0 and doing head gaskets on them takes patience and some know how, but once you get it down then every 4.0 OHV you see in the shop needs fresh head gaskets, lower intake, oil adapter o rings, timing cover, oil pan. etc etc.............. it really can buy you another 200-300K miles on these engines