Car will not turn over after a used transmission was installed

Here is what happened,

I have a 2002 Kia Rio, This car always would start right up with out even giving it any gas, Right away, every time, it would start, The tranny went out last year, I had a used one from a junk yard put in it, After the transmissions were changed out and hooked back up, The car would not start, Could this be a neutral tranny switch or safety switch problem? Because the car battery was disconnected for like probably 8 hours, and I think this car had a keyless wireless entry, At one time, But when I bought the car used, the Keyless wireless entry contols button thing, was not there, Or could my problem be a computer code? Or the the computer keeps getting reset? The last time the car was started, Below is what the guy done to get it to start.


INSTRUCTIONS FOR RESETING THE KEY, THE COMPUTER,
AND THE ALARM SYSTEM, IN MY 2002 KIA RIO

1.) Open the hood,
2.) Locate the diagnostics connector behind the Kia's battery,
3.) Open the cover on the diagnostics port,
4.) Connect a jumper wire to the connector,
inside the port marked "6"
5.) Connect the other end of the jumper wire, To the positive terminal,
on the battery,

6.) Sponsored links
7.) Enter the Kia,
8.) Place key in the ignition, Starting it as far as it will go without starting the engine,
9.) Push the lock button, On your key FOB, For 3 seconds, Until the lights on your dashboard
blink,
10.) Your key has been reprogramed, And your alarm and computer has been reset,
11.) Turn your Kia off, Remove the jumper wires and close the hood.

After the car was started, He told me to turn it off and try restarting, So I did and it started, Then he tucked this open end wire that was bare up inside my dash, I guess he thought it would be in the way of the the gas and break peddles, I got ready to leave and it was getting, So I turned on the headlights and the car stalled right away and would not start again using the method above, Please help, Deb