I bought a 96 Runner with the 2.7 4 cylinder in it this January for $3600, the truck had 145000 on it. I work at a shop so I inspected it before the purchase and found nothing alarmingly out of order, just a few regular service items that needed replaced.
Mileage for the first two tanks before I began to replace parts was about 15-16. Pluggs,wires, new airfilter and Mobil 1 Synthetic 10-30 oil change made for no change in mileage, however I did noticed better performance. Even after I installed 265/65/R17's with custom rims I did not notice any mileage gain. The only peculiar even was a roadtrip from Montana to Moab Idaho just after I had installed header and full exhaust (stock manifold was split in two, huge power gain, no mileage in town) I averaged about 23 MPG all the way down to Utah. I figured the motor just needed a good roadtrip to clean all the nasties out of the injectors etc. Return home and I'm back to 15-16. I purchased an MSD 6A ignition system to properly power the new 8.5mm wires I had bought and mileage jumped to 17-19 in town, as well as a very noticable low range power gain. 2-3 months went by and on a road trip I smoked a distributor cap, I don't mean I check it and the contacts were messed up, that sucker melted through and was firing outside the cap. I replaced the cap and was really nervous my ignition was going caddywompus, however it seemed to be working fine. A week later I was trying to reroute the power to the MSD from my stereo lead to another switched 12 volt source, I had just installed an amplifier for my speakers and was getting timing noise from the speakers. I routed the lead to the cigarette lighter which was my next best source. After that I the MSD went caput. I just sent in the box to MSD but now I am bugging about mileage again, I know I should be around 18 stock. The only remedy I can think of is to try a fuel filter, however I have been to lazy to get in there and do it. If anyone has any other suggestions or past experience with a similar problem please share with me, I am a poor student, so I'd love to fix this problem.

 

you might try some seafoam.

 

I'm a little confused when you say you smoked the distributor cap...the 2.7 has coil packs....no cap.

I changed my fuel filter a few months back (around 135k miles) and didn't notice any gain in mpg. I would suggest that maybe one of your o2 sensors is fouled up a bit and that could be the cause of the lower mileage, that is, unless they were replaced with exhaust upgrade.

 

I was going to suggest cleaning the throttle body and replacing the O2 sensor, and if it's not done, to change the PCV.