Yes sir. I'll try to make it a "short story". When I first picked up the 4runner almost 2 years ago, it had a very hard time starting cold and had an idle that seemed to vary with a very subtle hesitation in 1st, 2nd and 3rd... I may just not notice it in 4th and 5th.sounds like you are in the 22re rabbit hole. I have replaced cold start injectors before, but they never ended up fixing the problem I was chasing. what are your symptoms?
I can feel a slight irregular "poof" that seems to correlate with a subtle stumble at idle.
Its a hesitation/stumble while at a steady cruising speedAs far as the hesitation while shifting, I would look at the dashpot. It's job it to keep the idle up between shifts. If it drops all the way down to 750 between shifts this could be the problem.