Hi, If there is no problem with yield of DNA than go for gel/colum purification of DNA which will also get rid of contamination of phenol which hinders in down stream process. If you are getting three bands like undigested plasmid after precipitating is it possibility of self ligation. Instead of phenol pptn you can try simple Na-acetate pptn. Also check the color and pH of phenol, if there is a problem in phenol DNA will get degraded, and you will see smear of DNA on gel.
It has been worked on from various angles, but right now the mold variety and the genetics of the inhabitants including age factor are the main factors.