Can't find any decent pictures (Fiesta mk1/mk2? above), yours should look similar to this, and you should see where the shaft used to be situated against the linkage, as it will be rusty. When you push the lever into 1/3/5 it pulls the linkage backwards.
It's moved as it wasn't tight enough when you had the 'box out recently.
If you can move it back to where it used to be fitted it should be close enough, but if still struggling to get any gears , how I normally do them, is put it in 3rd, then slacken the 13mm nut so it moves on the shaft itself then tighten it up. (you need to move linkage forward/backwards on the shaft so you can get any of the 1/3/5 gears before you do this)