From a guy who has been down the gearing road (see my signature) and is fixing to go down it again, here are some thoughts.
The cheap and dirty way to go is to convert your CVPI to an LX drivetrain. 2.73 gears and whatever torque converter comes in LXs. LX torque converter stall speed is probably in the 1400-1600 RPM range. All the engineering is done and this is as cheap as mechanical projects come. Visit your local junk yard, find a 2.73 axle and a torque converter from an LX and swap them in.
If you are reliability bug like me, this would be a good time to rebuild your automatic. Make sure the cooler is good and the lines are clear and not kinked.
Slowing your engine down at a given road speed reduces the volume of ATF pumped from the transmission to the cooler and the transmission will tend to run hotter than your 3.55s. Heat buildup can result in spectacular (parts scattered down the road) automatic transmission failures.
All that said, you can gain 2.0 MPG by doing a manual transmission swap alone. A stick offers whole new vistas of hypermiling possibilities and maybe another 1-2 MPG can be had from improved driving without having to outfox your transmission. A stick will also allow you to reap additional benefit from any aero improvements you can make. If you enjoy rowing the stick, a manual is flat-out the most durable way to go long term. In an ecomodded car, a clutch should last a quarter million miles.
That said, a conversion to a manual is not for the faint of heart or short of resources. They don’t call this conversion a “sex change operation” for nothing.
But it can be done and has been done. Check out
Crown Victoria, Grand Marquis, Marauder, and Towncar. In their forums is a very thorough discussion of five and six-speed swaps into Crown Vics. Mechanically, Crown Vics and Mustangs are almost identical, so Mustangs are a fine source of parts. A number of guys have done this and are willing to tell you the short cuts.
A TR-3650 transmission from 2001 to 2010 Mustang should work OK for a ecomodder. A more durable and flexible option would be a T-56 from a 2003-2004 Mustang Cobra. Some T-56s come with a spectacular 0.5:1 overdrive sixth gear. (Imagine driving down the road at 70 MPH and turning only 1190 RPM or 1550 RPM with 3.55 gears) Unless you have plans for a supercharged 5.4 or 6.8 (V-10) a Tremec 6060 (aka T-56 Magnum) is overkill. That transmission is built to withstand torque that would snap the crankshaft of a 4.6 V-8. Tremec 6060s are used on Corvettes and Vipers but you can get bell housings for Ford engines.