The hole on the third switch you are refering about is the alarm's LED which seemed to be removed by the previous owner,the rectangular hole you also looking at is a missng cigarrette astray.
You can always have a nice parking brake,shifter & TOD handles installed that matches the VX's interior,also the gas & brake pedals to match the whole set.
If you want the cigar astray some one here might have one for sale or even free to you.
Also have a aftermarket alarm system installed if none is there