1993 Infiniti G20

I have an 1993.5 infiniti g20 when I first got it I had to replace the engine. Replaced with engine that was manual.

I am having the issue with my car where it acts like it doesnt know when to shift; I have also noticed when going down the road I feel the wheel wiggle left and right about 0-40mph. I know I need an alignment it pulls to the right.

It has the A/T Switch where you can switch between Power and Comfort Modes; I leave it on auto. Sometimes when it needs to shift the light comes on for a split second like a flicker, when I start the car I do know it needs to have that light turn on to signal good to go but it mostly just blinks about 16 times. I try to restart the engine but usually is the same. Also sometimes when I stop it luggs and just dies. It usually works fine about 40mph and above. Runs great when its not in fail-safe mode.

We replaced the VSS-Vehicle Speed Sensor, Drained the system, We have even reset the ECU (when I reset the computer it did blink a code but I think it was before the engine was replaced blinked 34 code; Which is Knock Sensor. Which I cleared.

i have done the onboard diagnostics without consult and it has to do the 10 blinks it, It has done 2 different ones at couple different times:
X-0-0-0-0-0-0-0-0-0-0 and X-X-0-0-0-0-0-0-0-0

The OD light does not blink at all, SES check engine light is not on.

I have the FSM for a 1994 infiniti g20