Preheat smoker to 225℉ with your choice of wood or pellets. Place the whole jalapenos and habaneros (if using) on the grill grates, close the grill lid, and smoke for about 1 hour. Remove the peppers from the grill to cool.
When the peppers are cool enough to handle, cut off the stems and remove the seeds and pith (inner white rib part). Then cut the peppers in large chunks. Do the same for the two bell peppers. *See notes.
Add all of the seeded peppers to a food processor. Use the pulse setting to process the peppers until they are finely diced. *If you don't have a food processor, you can use a knife to very finely dice the peppers.
Add the diced peppers to a piece of folded over cheesecloth. Fold the cheesecloth around the peppers, and squeeze to remove any excess moisture so that your jelly sets up properly.
Add the diced peppers to a pot with the sugar, apple cider vinegar, salt, juice of one lime, zest of ½ the navel orange, and juice of ¼ of the orange. Mix together well. Bring to a boil, stirring frequently. Then, reduce the heat to a low boil and continue to boil for another 10 minutes.
Slowly stir in the liquid pectin, boil the jelly liquid for another 1-2 minutes, then remove from the heat. Cool for 5-10 minutes, then pour into mason jars and screw on lids tightly. Depending on the size and number of your peppers, you should be able to get 3 pint-sized mason jars.
Flip the jars over and allow to cool upside down on the counter for 30 minutes to 1 hour. This helps to evenly distribute the pepper pieces. Then, flip the jars right-side up and cool at room temperature for another 4-5 hours.
After the total 5-6 hour cooling time at room temperature, transfer the jalapeno pepper jelly jars to the refrigerator. Refrigerate overnight, and your jelly should be fully set and ready to serve the next day.
Serving suggestions: Spoon one pint of the jelly over a block of cream cheese (or smoked cream cheese) and serve with buttery crackers. Use the jelly as a deli sandwich spread. Use as a glaze for smoked ham or pork tenderloin. Baste onto ribs or grilled chicken about 15 minutes before done cooking.