So I have a 2004 rx8 with 172,000 miles and 150 miles on the motor and makes good compression. Ignition system is brand new along with new fuel pump and new injectors. The problem with the car is that every single time the key is shut off, it looses it's memory for the fuel trims, essentric shaft plate postions, etc. I had just put the motor in the car after having it out for a good month (waiting on parts) and this problem started right after that.
When the key is turned on, the guages do an erratic sweep going up then down. Once the car starts, it runs similar to when you do the 20 brake stomp in 8 seconds. By that I mean it has a rough idle and almost stalls and then picks up untill it finds where everything needs to be to have a smooth idle. Once the car figures itself out after some time, it runs perfect and has a smooth idle. Also, the memory for the keyless entry is gone and the car won't hook up to an obd scanner that has prevoiusly worked on this vehicle.
No sure what could be causing this, that's why I turned to this site to see if anyone had any ideas. I go to college at unoh in lima ohio and time for me to work on it is limited due to me being 4 hours from home where all my tools are. Any help would be greatly appreciated

 

Make sure the battery cables are secure and in good order and leave the battery disconnected for a while and see if the ECM resets. If not, you will need a trip to the dealer.