Adil, if the Colonel does not mind, I would like to pay him a visit and check out your FJ when I go to Islamabad next.
Also, about the carb/tune thing, like I wrote in that post of mine, once you have all the jets and float level set to factory spec and are certain that there are no vacum/compression leaks, you should try to tweak the carb judging from the color of the plugs going in and out 1/4 turn increments. For that however, you need to have plugs that have the same heat rating as the OEMs. I believe Denso W14EXR-U and NGK B-5ES are what you will find recommended in the factory service manuals. However, I have not found these in our local spares shops. Incorrect heat rating spark plugs will cheat you with the wrong colors leading you to make incorrect assumptions about your mixture.
I saw you had moved up to a different ignition coil. Depending on what kind of volts it pumps, if its stronger than the OEM coil, you should try and increase the gap to a tad over 0.032in (factory setting). That will make the coil work harder but will give a longer 'spark front' for the mixture to ignite in the cylinder. Should make it run sweeter. Be sure to gap the plugs with that plug gap disc, not a feeler gauge.
Also, I think if you are keen on mileage, the move to the H55F was a good one. It will give you better O/D in fifth (250-300 RPM lower) hence marginally better economy. If you really want to feel a change, go for 3.73 diffs if you have 4.11s in there right now. They will not only make it go alot better on the highway with an additional 150-200RPMs to spare, but will also make it rev less in the city and save gasoline.
I was curious, are you using the OEM thermostat? If so, where did you find it from? I need one for my FJ but the ones I have seen are all too cold at 82'C. Need a 88-92'C for my FJ.