Fill up a stock pot about halfway with water and bring to a boil. Do step 2 while you are waiting for that to happen.
Remove all of the stems from tomatoes. Fill up a clean sink with water and dump all of your tomatoes in. Swish around and drain.
This step will need to be done in separate small loads. Add about a quart of tomatoes at a time to the boiling water and allow to blanch (boil in the water) for 30 seconds to one minute. While you are waiting for the first load to finish, put some ice in a big bowl and fill up with water. Set on the counter near the pot you are using for the tomatoes.
With a slotted spoon, remove the tomatoes from the boiling water and place them into the ice water for a couple of minutes. This will stop the cooking process. Remove from the ice water and place in a bowl for later. Repeat Steps 3 and 4 until all of the tomatoes have been blanched, cooled, and moved to the bowl for later.
With a knife or a tomato corer, remove the stem end and slip the skins off the tomatoes. You can use the scraps to make tomato powder later if you have a dehydrator. At this point, you can cut your tomatoes into halves or quarters, or leave them whole.
Dice tomatoes into 1/4-inch pieces.
Remove stems and seeds from jalapenos and dice those too. (Use rubber gloves just for good measure.)
Dice the red onion.
Pour boiling water over chili peppers just to cover, then cover the bowl they are in for about 15 minutes to steep. Drain half the water off and puree chili peppers until smooth (about a minute).
Combine all ingredients in a large saucepan and bring mixture to a boil over medium-high heat. Reduce heat to a simmer and allow to simmer for 10 minutes or until thickened.
Fill your hot jars with salsa, leaving a 1/2-inch head space. Remove air bubbles with a bubble remover, and clean the jar rim.
Center the lid onto the clean jar rim and screw on the band only fingertip-tight. Repeat steps 6-9 until all jars are filled.
Place jars into the simmering water in your canner. Water must cover jars by at least 1 inch. Adjust heat to medium/high and cover the canner. Wait until the water boils. Once water is boiling, set your timer for 15 minutes.
Once processing time is finished, turn off the heat and uncover the canner. Allow canner to sit for 5 minutes, then remove jars with the jar lifter to a towel on your counter. Allow to cool for 12 hours. Test seals, label, and store jars