A few things, tkcomer:
1) My interference issues came from using the Clifford intake in conjunction with the Borla header. Your header downtubes may not stick out as far as the Borla.
2) This Clifford intake is for a 258. I don't think they make one for a 4.0 because it had fuel injection from the factory. Prolly not much of a market for intake manifolds designed for 4.0 heads and a carburetor.
3) The Clifford intake has a big square opening and plenum designed for a 4bbl. If you plan on keeping your Weber, my guess is the gains would be minimal if there at all. You might even lose some bottom end due to the large plenum design.
4) I don't know what profile your cam is, but consider that all parts should work toward the same end. I have a very mildly aggressive Crane Cam (260H) that is designed to bump the midrange and open up the top end without losing too much bottom end.
You want to make sure that your carburetor is sized properly for what you are trying to accomplish. You can calculate what CFM carburetor you want to run by doing some math with displacement, the max RPM you will turn, and the volumetric efficiency of the engine. Don't know what my (or your) VE is, but 85% (0.85) will get you in the ballpark. A quick Google for carburetor CFM calculator turned up a few. When I ran 258cid, 5000rpm, and .85VE, it put the 390 in my neighborhood.
My engine does NOT run like a 6 anymore. It doesn't have the bottom end of a V-8 or a 6 that's been really tuned for stump-pulling, but it's smooth all the way down to just below idle. Get her above 1500 and she is already pulling stronger than stock, and anywhere above 2500 she just flat out howls.
So, the answer depends much more on what your cam profile is and how much you like your Weber. Webers are friggin sweet. I had one on my stock 258 and really liked it. If your cam focuses on bottom end, you probably want to stay with a stock (smaller runner, higher velocity, less volume) intake manifold and your Weber. If you want to sing at the higher rpms now and again and your cam does too, then a big intake and small 4bbl (or BIG 2bbl!) may be for you.
Keep in mind that your exhaust plays into the picture too. The Borla tubes are pretty good sized, and I have a large pipe with no cat. Basically smaller holes (carb, intake, and exhaust) and shorter durations mean more velocity --> better low end grunt and you run out of breath sooner in the higher rpms. Larger holes mean more likelihood of flopping around in the low end, and a lot more power and room to breathe up top.
If you didn't already know some of this, I hope it helped. There's a lot more knowledge/crap where this came from. I'll be glad to share if ya wanna know!