You can also test if it's mechanical fault in transmission or electrical fault in transmission control circuit with this test (copy&paste from service manual):
MANUAL SHIFTING TEST
HINT: With this test, it can be determined whether the trouble
is within the electrical circuit or is a mechanical problem in the
transmission.
1. DISCONNECT SOLENOID WIRE FROM TRANSMISSION
2. INSPECT MANUAL DRIVING OPERATION
Check that the shift and gear positions correspond with the
table below.
Shifter position Gear position
D O/D
2 3rd
L 1st
R Reverse
P Pawl lock
HINT: If the L, 2 and D position gear positions are difficult to
distinguish, do the following road test.
• While driving, shift through the L, 2 and D positions.
Check that the gear change corresponds to the shift
position.
If any abnormality is found in the above test, the problem is
in the transmission itself.
3. CONNECT SOLENOID WIRE
4. CANCEL OUT DIAGNOSTIC TROUBLE CODE
Is your car GE or GTE? This test is for a340e transmission with 2jz-gte, not sure if it works with 2jz-ge engines...?