The following are my beliefs only, based on more theoretical knowledge than first-hand factual experience.
1) There is no one magic bullet to economy. For more, see the tornado swirling device thread of a month ago.
2) Economy is about combustion efficiency and the transference of this force to do work.
3) Sometimes, an engine built for speed and one for economy share identical goals and make nearly the same power.
Now, since you probably took some physics, you know how a system is comprised of many parts. The engine will thus be part of a system, that is unless we are simply going to run it on a dyno, in which case it will be the only system.
If it will go into a vehicle of some sort, you will need to integrate it as best possible (with gear ratios for economy, etc.). If it isn't, you will not worry about it.
So, what makes an engine efficient? These are my ideas..
As I stated above, it all hinges on combustion efficiency. The faster the charge can be made to burn, the more potential exists for optimum power production from a given unit of fuel.
Why is burn rate important? Timing! Anyone who has timed an engine knows you must set the ignition to fire sometime prior to TDC. This is to get the fuel/air mix ignited prior to the power stroke, so as to generate the greatest cylinder pressure during that time. However, it does not take a very astute person to realize that power expended on the upward (compression) stroke of the piston, is work in the wrong direction. Thus it could be termed, "negative work" which is being done prior to the power stroke proper.
It should now be apparent that we would like to limit the amount of "negative work" being produced. Additionally, it would be nice to be able to use some of the work which was previously being expended on the compression stroke for power production on the power stroke. The only way to do this, is to increase the rate of combustion. A faster burning charge will not have to be ignited as early in the compression stroke to reach the same pressure levels on the power stroke, and thus the engine will make more power for a given quantity of fuel/air mix and speed.
So how do we increase the rate of combustion? Let's start with airflow 'quality' (as it's been termed).
When most think of airflow, they think of quantity, usually thinking the more the merrier. This is basically OK for an engine built for speed, but we are not, so assuming sufficient quantity, quality will be of priority.
At some point in the induction process, fuel will be introduced to the incoming stream of air. This fuel must be administered in as atomized and homogenous a form as possible. This level of atomization MUST be maintained up until, and through the time of combustion. This is because fuel which separates from the air, or otherwise clumps together, will not burn as quickly as fuel which is finely atomized. Put simply, liquid fuel will not burn! Throw a match in a bucket of gasoline and see what happens some time.
To keep fuel from separating, you must pay careful consideration to the ducting design. As air flows through a port which turns, the air will "hug" the inside radius of the turns. If you take a string and pull it through a port, the line you see represented will be a very close approximation to the way the air is flowing. When the air tries to do the above, you will have a distribution of pressure throughout the port. Thus, if you were to slice a cross section of the port through a turn for instance, you would find that the air pressure along the short path would be substantially lower than along the "long side" . This has a tendency to create shearing in the flow as the velocity will also differ with the pressure. All of the above causes the fuel to be drawn out of the flow stream.
To solve the above problem the ducting will have to take on D or trapezoidal shaping, with the short paths being widened and the long sides "shrunk" to help balance the pressures.
There is another problem with air/fuel mix which you should know about also. Fuel is obviously heavier than the air which is carrying it. If you encounter a turn, the fuel will try to go straight by means of it's inertia, while the air will seek the lower pressures encountered on the other side of the bend. It can help to increase the size of a duct through a turn to counter-act this effect. The area will need to be decreased again on the other side of the turn.
I will also add that the area just before the valve seat should always be smaller than the rest of the port and this area should be between about 84-92% of the valve diameter. I'll let you figure out the rest.
The last consideration is port wall lengths. The larger the difference in length between each portion of the port, the bigger the difference in surface "friction" imposed and the greater the chance of sheering and subsequent fuel separation. Thus the port floor, roof, and walls should measure the same in all cases. You will find this difficult to do, but do not forget this point, as it makes design and modification easier to understand, do the best you can.
The last big bugaboo prior to the combustion chamber are the seats. All I can say is that the seat is extremely critical to not only airflow quantity, but quality as well. Keep the length differences noted above in mind and carry that ideal all the way to the seat itself. The long side of the port should have virtually no bottom angle (nearly straight from the guide, shortest wall length) with the short side as generous a radius as possible right into the seat (longest wall length). Don't go hog-wild on a top angle, something like a .010" 15 to 30 degree (or less) is best in nearly all cases. This is something you could take a long time developing, so just keep the top angle minimal.
We now find ourselves in the combustion chamber and I will say that two things are important. One is turbulence, the other is surface area to volume at TDC.
Turbulence should always be oriented (not random) and should always be in the direction of swirl as opposed to tumble, which is a random form (in my opinion). You want the swirl to make about two loops of the combustion chamber, which you can figure out by using an RPM reading swirl meter and about two years of time spent making calculations to relate flowbench results to actual running conditions. Suffice it is to say, you won't spend this time, so think about the following. Since you'll be making your own cam and follower design, you now have the ability to very the timing between both inlet valves so as to start one opening prior to the other. This can be used to introduce a bias to the flow, and thus swirl. Also consider lift for this. I'd make a guess of 5 degrees timing difference and about .030" lift difference. Try it and see what it likes if you have the time to do it. If you don't, just go with everything else I've said and forget about it.
Combustion chamber design will also influence the flow, walls placed near the valve can cause the flow to do all kinds of screwy stuff, so try to keep everything at an equal distance if you can.
Lastly, you need to consider how the charge will be confined at TDC. You would like the charge to be "pushed" to the exhaust side where it will be heated to a point where it will burn faster. The spark plug should also be in the vacinity of the exhaust side for proper combustion. This is very important for the mixture to burn quickly and efficiently. You can achieve this effect by placing a pent-roof dome on the piston that will 'quench-off' the intake side of the combustion chamber, and thus force the mixture to the exhaust side. Since you will be designing the head, you can put the spark plug (or better yet, plugs) on the exhaust side, and the heat, combined with their placement will work for you.
Lastly, you need to get the exhaust out quickly. Exhaust residue in the chamber will slow the rate of combustion, which is not what we are after! Exhaust seats should be full radius, but with a 45 degree seat. Try a steep back angle on the valve (35 to 40 degrees works best usually). All the rules of inlet port work apply to the exhaust, but you might consider making the port no larger than the exhaust valve throat, or possibly even smaller for best velocity. Obviously wave tuning is important, but I'm somewhat 'green' regarding that.
Lastly, smooth doesn't mean anything to the airflow. I would texture the inlet ports with no less than 60 grit sandpaper on a split rod, scratches perpendicular to the direction of airflow. 80 grit is ideal for the rest of it, chamber and exhaust ports respectively.
I'd look at the modern crop of Honda engines for a good idea of how things are evolving. Try to keep the valve angle shallow for the minimum chamber depth and the lowest piston dome that will achieve the above mentioned ideals. You may have to run something like 12:1 or higher compression to effectively quench off the inlet side, and I wouldn't worry too much about doing it. You may also find you need relatively short intake cam timing to keep the inlet valve reliefs as small as possible, don't worry about it. You care only about combustion efficiency, so beyond airflow quality, quantity can take a back seat for awhile.
Good luck, have fun.
Sean