Tuned Length Intake Runners
Just like on the exhaust side, there are torque gains to be made simply by making the intake runners the appropriate length. With side-draft carbs it's fairly easy to modify the manifold or even make a new one from scratch, though with a downdraft you might just be stuck with what you've got. And anyway, with downdrafts it will be difficult to make the runner lengths anywhere near equal.
Basically a low speed engine will want very long runners while a screamer will want them very short, and obviously there is an infinite range in between. There are formulae to calculate the ideal length, or alternatively one of the engine simulation software packages (eg. PipeMax) can guide you. Keep in mind that the length includes the intake port in the cylinder head. While the correct length can provide substantial gains it's not absolutely critical to get it right down to the last millimetre - if its within say 10mm you'll get close to the best possible performance. If you use something like PipeMax you'll find that it suggests several different lengths depending on whether the runners are tuned to the second, third or fourth harmonics. For example it may suggest lengths of 21", 14.6" or 11.5" for a specific combination. For best output it's usual to choose the length corresponding with either the second or third harmonic but often the deciding factor is the amount of room available. With injected engines this isn't so much of a problem as the runners can be simply coiled up (as with many OEM manifolds) to save space. Obviously though this isn't such a good idea with carburettors. As a very rough illustration a quite mild street engine with a torque peak around 3000rpm will like a very long runner - up to about 400mm or even longer. A hotter engine with a torque peak at say 5500rpm will probably want a total length of 200 - 250mm, while a hotter engine again will want a total length of only 150 - 175mm (and remember this includes the head). High revving engines with triple Webers may well benefit from experimentation with slightly shorter runners than are commonly used.
The actual optimum length for a particular engine depends on a variety of factors, and so should be calculated either manually or using software rather than just using a figure that worked on someone elses engine.
Port Matching
Careful matching of the manifold ports to the cylinder head ports can help prevent flow losses at the head/manifold interface. It sounds simple enough but there are a few things to keep in mind. Firstly, be wary of using the often recommended method of using the gasket as a template to mark out the ports. The gaskets are often a bit oversize so you can end up with a short section of the port on either side of the joint where the port area needlessly increases before reducing again. Obviously this won't do much for flow. The other thing to watch out for is accurate location of the manifold - it's pointless making the ports match exactly if the manifold can move around and you can't see whether the ports are aligned. Things like alignment dowels or extending the locating lugs will help here, and you can check the alignment by using a blank gasket and thinly smearing the head and manifold faces with bearing blue to indicate the mismatch.
Where the manifold runs into the head in a fairly straight line it's best to match the ports exactly (provided of course that it is accurately located as well) or else make the manifold opening just a little smaller than the head opening - a step-out of around 0.5 to 1mm all around is OK. If there is a curve in the runner at the gasket joint - as is common with downdraft manifolds - try to have a 1mm or so step-out on the long or outside wall and match the others as closely as possible, but whatever you do avoid creating ledges or step-ups going into the head. It's always best to have the manifold slightly smaller if it can't be matched exactly.
The techniques above apply mainly to applications where performance is the primary goal; on a mild street engine I wouldn't worry too much about getting a perfect match. And if fuel economy is the goal, then a small step up into the head port is actually beneficial. A small but sharp-edged step won't reduce flow that much but it is very effective in shearing any wet fuel that has collected on the runner floor back into the airstream, and may allow the use of slightly leaner jetting.
While we're talking about the manifold to head joint, we may as well take a quick look at the angle of this junction. With both the 9 and 12 port heads the port floor rises fairly sharply, so if it's possible you should try to have your intake runner approach the head fairly horizontally (as with the factory 12 port manifolds) or even sloping upwards very slightly. Many aftermarket manifolds slope down into the head, and this isn't good for either flow or fuel separation. Lowering the approach angle may introduce exhaust clearance issues but if it's at all possible it's worth a look.