1az-fe to 2az-fe engine swap RAV4 overdrive/high gear not working

hi all, i had my 2004 rav4 cruiser blow its motor a month ago due to living in
the remote bush all i could get was a 2 AZ-fe 2.4L motor out of a camry , all
went well as it could other then the top right side engine mount not being the
same and it having a totally different knock sensor as i had to use my wiring
harness out of the 1AZ as all the ECU plug are different on a Camry and the
throttle body required a diffrent length cable so i put the 1azfe throttle on it  ( i
gather the 1azfe throttle is a little smaller intake but i figure that only going to
make it run lean on air or fuel

now it starts and runs fine but it does have a vibration but i cant blame it as
its missing a engine mount and i am waiting on a replacement to arrive ,

my problem. it seems to 90% of the test drives wont go into top gear and the
second it suppose to go into overdrive/top gear the engine light comes on,
some times it works fine but rarely, i am only doing small test drives after i try
different things as to not harm it

possible causes-  i can think of but i want confirmation and other ideas as the
gearbox was fine until i replaced the motor and it does shift intermittently into
top gear

- transmission is a little over full i should drain it but i have never had a car
react like this over some excess fluid
- i left the knock sensor disabled as the 2azfe one has more wires and and a
different plug and the old 1azfe sensor connect totally different
- i fucked something up when i joined the gearbox to the engine block eg.
torque converted bolt is loose or i damaged the torque converter when i was
trying to meet it to the motor
- another 2azfe sensor that plugs into my wiring harness is different internally
and causing the car to not got into top gear or not triggering a condition in the
ecu as it should
- tilting the gearbox during fitting it has caused gunk or something to clog or
block a transmission solenoid or fluid path


i would like to get some ideas i am solo with limited tools and resources due
to living in the bush and anything that could narrow down my problem or help
would be awesome

also i cant read the engine codes i have ordered a cable from china but god
knows how many months it will take to  arrive and i need my car going to
access doctors and get food i purchased a quality obdII scanner only to be
told toyota use there own cables and software on a obdII plug to fool us mere
mortals into thinking there obdII compliant