Don't let the bad results obscure the problem. A 2.41 axle ratio will give better mileage than a 3.73. An overdrive will not deliver as good a mileage as the 2.41 axle will in direct drive if its overall final drive ratio is the same (ie a .646 overdrive x 3.73 axle ratio = 2.41) because the overdrive mechanism wastes at least 6% of your engine power.
I think that what is happening is that your manifold vacuum is so low that it (1) prevents the transmission from shifting properly and timely to the correct gear (2) your carburetor's "power jets" or equivalent are opening and enrichening the mixture (3) the vacuum advance isn't enough to give the correct spark advance for to produce that torque at your current rpm.
It sounds like you have done a lot of modifications to your vehicle. Most of these modifications are planned to enhance power and accelleration at the expense of every other concern.
Put a vacuum gauge in the car. It will show you when your carburetor decides to go to a richer mixture, whether it is by opening jets, secondaries, or whatever. It will also show you how uneven the demands for power are placed on your engine.
Look closely at the exhaust side of your car. Anything that prevents the exhaust from getting out freely is not only causing a horsepower loss (the power lost by pumping against that resistance) but is preventing the engine from being able to suck in that nice cool lean mixture and producing intake vacuum.
A side note. If you keep your rpm below 2000 you can get by with ridiculously little muffler. I once ran a Mercedes diesel for about two years without a muffler just by keeping the rpm down so that I wouldn't be a pest with the noise.
If the axle ratio to produce optimum mileage for your vehicle is in the low 2s (and I believe that it is) the optimum transmission to produce mileage is a wide ratio manual (6.32 or 6.69 are both very appropriate). As a driver I would appreciate a 5 speed, but as an engineer, I can't say that it will produce much of a mileage gain. The manual will eliminate the current problems that you have with shifting, but you will have to train yourself to use it. A transmission is the tool that you use to tell your engine how hard that you want it to work. To accelerate faster, tell the engine to work harder by running higher rpm. To get mileage, keep the rpm down.
By using a manual transmission you can even make a combination that only has to be fed when you make it work. A car with a 6.32 transmission and a 2.41 axle will move off the line just like a car with a 2.41 first gear and a 6.32 axle, it will just have more of a loss of power during the shifts.
For mileage you have to keep the tire pressures up, whereas someone with a drag racing background might want to run low tire pressure to get better traction. This little bit of extra acceleration hurts you all through the driving cycle.
If you are a good racer, you keep the wheel bearings and universal joints well greased, the chassis aligned for minimum rolling drag.
You might want to think about your thermostat. The engine has to be up to proper temperature to get the best mileage, though this effect is slight with carburetors and very noticeable with fuel injection, which changes the mixture radically when you get to normal operating temperature.
Finally, be realistic about what you expect from your car. A Mustang with 302 could be expected to get 25, but if you get that Malibu to 22 you have done well.
One last thing. The road from San Antonio to College Station has lots of long hills. Don't fight the hills, and especially don't use a cruise control that fights them by opening the throttle when going up and closing it when going down. Hold a steady throttle. Lose a couple of miles per going uphill and gain them back going down. Just try to keep your throttle steady.
I wish I had seen your posts six months ago when you had the problem.
