In LFS. Put the shifter into the neutral position. Go to Options -> Controls. Click on the "Shifter" button to the right of "Axes/FF". Under the "Wheel buttons" column, click on the button to the right of "First". Now put the shifter into 1st gear. You should now be able to use 1st gear. Repeat for 2nd-6th + Reverse if necessary.
edit: Attached a screenshot showing what your options should look like.