In two small bowls, put minced jalapenos in one and minced cayenne in the other. Add just enough vinegar to cover peppers and put in refrigerator overnight for the best flavor.
In a large, stainless steel saucepan, combine chopped and sliced peppers, pepper flakes, cider vinegar, and sugar. Cook over medium low heat until peppers are very soft and vinegar mixture is fully incorporated with pepper flavor, about 1 hour.
Strain vinegar mixture through a fine mesh sieve and discard pulp and seeds.
Return strained vinegar to the saucepan and bring to a boil. Stir in liquid pectin; continue stirring constantly and bring back to boil for 1 minute - no longer! Remove from heat and skim off foam.
Divide jelly mixture and add red food color to one mixture and add the minced green jalapeno peppers. To the other half of the mixture add the green food color and the minced red cayenne peppers.
If you like the golden color of natural pepper jelly then combine the minced red & green peppers into the jelly mixture.
Using a canning funnel, ladle jelly into sterilized jars. Seal, and process in a boiling-water canner for 5 minutes. While jelly is cooling occasionally turn jelly upside down or gently shake jars to keep the minced peppers evenly distributed in the jelly until it's set.
TIP: Sterilize your clean jars and lids in the oven. Place on a baking sheet at 250* F for 20 minutes, then turn oven down to 225* until all jars are used.