for positioning the box there's a small knob on the base of the box and a dimple in the column, no adjustment in where it mounts, but it looks like your rods from the box to the trans may be coming thru the clamps a bit too much - which could make the forks in the box not centered straight up
if it's not going thru the gears smoothly, loosen things up and get the arms on the trans in their neutral position, then the forks in the box straight up with the shift lever in neutral, that will position the rods in their clamps .... also check the adjustments in the shop manual [sect 7-4] for positioning the shift lever knuckle at the top of the column ... cinch it all down
and get out there and drive'er!
Bill
