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have you changed the coolant temperature sensor? there should be two wires running out of it. the one with one wire is just for the gauge.
I believe the the crankshaft sensor is for the non-dizzy v6's. I looked on my 94 3L around the crank pulley & I have no sensor there. What kind of plugs, wires, cap, rotor you put in? I would start by checking everything you did for a tune up plug gaps, bad wires & so on. If you have a EGR on it like I do, check those 2 small hoses and the egr tube for any damage.
Check for intake hose leaks and vaccum leaks. When did you change your fuel filter last? Dirty injectors are possible. The sensor you replaced is the engine coolant temp sensor & the other one is for the cluster. It could be a bad ignition coil to. Did you reset the computer when you replaced those sensors?
I had a problem like this on my old 88 2.3 it took forever to find what it was. Inside the distributor cap had a small crack and moisture got in there and would sputter in the first couple of gears. After it warmed up it would go away. I installed a new cap and problem solved. I double check stuff like that when I am working on my 94.
Check for exhaust leaks around the manifolds.
I'm out of ideas? I will try and talk with a few Ford mechanics I know to hear what thier thoughts are.
I just re-read thru the whole thread & did not see anything about the idle air control valve or throttle position sensor. Have you checked those?
Fuel Pressure test? Fuel pressure regulator? did you check/replace the ECT?
From your posting I take it that the truck sutters until it warms up a little (under 10 minutes). It sounds as if the higher the humitity and the cooler the engine the more you have an issue. When you leave work in the afternoon it runs well from the start. If I have this correctly, I would bet coffee on you having moisture in the cap. With a good fitting cap, condensation can remain for quite sometime, take the cap of when it is cool and early morning and check for the smallest amount of moisture.
This is your ECT (enging coolant temp sensor). The idle air control valve is on top of the plenum by the spring for your throttle cable. It's a silver cylinder looking thing.