Slice tops off jalapeño peppers, cut in half lengthwise and cut crosswise in half. If peppers are larger and have a lot of white membrane, remove some from the top half of the peppers if desired. Use gloves to protect hands if your skin is sensitive to heat. For a milder version, remove all membrane and seeds.
Add peppers to food processor and chop until quite fine. Take care not to breath in the fumes.
Add peppers to large pot, along with mustard, sugar, honey, vinegar and salt. Slowly bring to a low boil, stirring often. Boil for about 3 minutes.
Whisk together flour and water until smooth. Carefully whisk into hot pepper mixture and continue to boil for about 3 more minutes until very thick and all flour is combined well. Stir continuously to prevent scorching on bottom of pot.
Remove pot from heat. Carefully fill clean sterile jars, leaving about ¼ inch space at the top. Wipe rim to ensure no mustard is on jar rim which could interfere with the seal.
Add new seals and rings to jars. Tighten lids gently without over tightening.
Fill canner pot or other large pot with enough water to completely submerge jars. Bring to a boil.
Add jars to canning rack and lower into canner pot. Process for 10 minutes. Remove to a towel lined counter to cool. Process jars in batches as necessary so they aren't crowded or touching in rack.
Alternatively, instead of using a canner, use tongs to lay a dish cloth in the bottom of the pot. Carefully lower jars into pot on top of cloth to prevent contact with bottom of pot. Boil for 10 minutes, then cool on counter.
Check lids for seals, hand tighten rings if necessary after cooling. Store in a cool dark place.