I have a 2002 Honda. Accord EX with a 2.34 cylinder V tech. The engine was bad, found a very clean super. Low mileage engine dropped it in now. For some reason, the transmission is shifting really weird. It is a couple seconds to go into reverse. All the lower gears are shifting really hard and slipping. I'm pretty sure all of the solenoids are plugged in correctly. I don't think any of them can be plugged in to a different position. Anybody have any ideas before? I pull my hair out. Thanks for any help

 

What was the failure mode of the engine?
Was the transmission shifting fine before?
Verify the transmission is full of ATF.
I prefer to keep the trans filled at the upper limit. But I live in a hillt area with off camber turns.

When the engine was replaced did you reuse the original engines ancillaries, sensors and harness?
JDM intakes, harness, and sensors are not always the same.
98/99 harness/sensors are slightly different than 00-02 models.
There are slight differences between the A1 and A4 engines.

Honda still used a speed density system which is robust but not the quickest when it comes to self diagnostics and may not set a code for faulty components. TPS can be bad and not set a code. TPS is one of the main sensors that will affect transmission operation.

Transmission functionality is greatly affected by engine running condition.
Hondas PGM-FI may be trying to operate the transmission correctly but the input sensors may be faulty giving an incorrect input which leads the PGM to give incorrect outputs.

If the transmission was working properly before the new engine it should work properly after the replacement engine. Verify all sensors are plugged in, operating correctly, and no damage to the harness along with no missing grounding or bonding wires.

And verify the battery is fully charged and the charging system is maintaining operational voltage.
Low voltage will cause issues.