No, you can't just pull the sector arm off and reposition. If you would have looked it does INDEED have a master spline. The misaligned part is the sector gear and shaft! the forward gear is a double, the aft gear is single. and the ballnut is in front. Ballnut aft side has teeth, it engages front of double sector, aft of double sector engages front of single sector. The service manual has the procedure where you count the teeth to mesh front sector to aft sector.
So.. it starts instantly and runs very smooth and you want to 'upgrade it' to 12v..... whatever.. your machine. I'd quit fixing it unless it was broke.. IMHO...
What clutch mod are you refering to?
For painting, I'd sand or abrasive pad off the rust, then prime, then paint.