If it's the 2.6 fuel injected could be the EGR is stuck. When cold the EGR vacuum circuit is bypassed by a thermo vacuum switch. Once the engine warms the switch opens allowing vacuum to the EGR. Then again it could be the thermo vacuum switch is stuck closed not allowing vacuum to the EGR, but then again it could be the O2 sensor, carbon buildup on the throttle body, timing, mass air flow sensor a vacuum tube with a hole in it or pulled out of place, low fuel pressure... That's what I love about these engines. You have so many choices!

My vote would be EGR circuit. Getting all the vacuum tubes back to the right ports after a tear down is easy to mess up; especially those
two on the thermo-vac valve, tough to get to with two index fingers. And if you haven't replaced the O2 sensor in a while it might be worth the twenty bucks. I recently went through the same scenario and while cleaning out the throttle and tuning/timing made a difference it didn't really start running well until I replaced the O2 sensor. I don't think they last 90,000 miles like the book says.