Replaced Motor, but hesitates during slow acceleration

Hi guys, I am a newbie, and guess what? I have a problem.
My friend has a ’92 Accord (f22 motor w. auto. trans.) and needed a new motor. So we found one and put it in. The newer motor has great
power, fires right away and for the most part, runs great.
There is however a little problem: when you drive it normally (by that I mean slowly accelarating from a light) as soon as the engine shifts to 2nd gear, the car almost dies, sputters and backfires in the intake. After the episode, the car is fine until you stop it, and let it rest for a while, then it comes back.
I replaced the EGR valve, O2 sensor, coil, spark plugs (new) cables and flush the efi system. No change.
There is another odd thing that might be related. When the engine is shut off, the fan kicks in, but the temperature is no where near requiring the fan to kick in.
Did I forget to connect something? I checked all the vacuum hoses, wire connections and I can’t seem to find one disconnected. Is there a sensor on the radiator I forgot? (i remember plugging the 2 fans, that’s it) Is there a sensor on the new motor that is deffective? (I kept all the old ones from the motor)Any ideas?
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