First, just to touch on several points about boiling water canning:
- Boiling water temperatures will kill all fungi, molds, and bacteria. It will not kill bacterial spores, specifically botulin spores.
- A high acid liquid will prevent those spores from germinating and multiplying. For these purposes, high acid is a liquid with a pH of 4.6 or less (the lower the pH, the more acidic). That's why you don't need to use a pressure cooker when canning high acid foods.
- When it comes to acidity, tomatoes are on the cusp. Most tomatoes have a pH less than 4.6, but a few do not. The University of Illinois tested 55 varieties of tomatoes and found that 15 of them had a pH higher than 4.6. The tomato pH depends on variety, ripeness, and many other factors. Bottom line, you really shouldn't take a chance when canning tomatoes, the odds will eventually work against you.
I've come to the conclusion that so much lemon or lime juice is simply not necessary, and small changes in the recipe are not problematic. Peppers and onions have some acidity, although not as much as tomatoes, so they really aren't going to change things that much. But the real reason not to worry is because the lemon juice that you add actually contains more acidity than the tomatoes, so small changes in the composition of the salsa will not affect it's pH much at all. From the research that I've read, a recipe that calls for two TB per pint has so much margin of safety built in that you could use as much pepper and onion as you do tomato, and the salsa would still have a safe pH.
Then there's the question of whether you must use a standardized lemon juice like Real Lemon or if you can use, well, real lemons (or limes, which are the same acid-wise). I used fresh lemons in the marinara and fresh limes in the salsa. This blogger tested a number of lemons from the supermarket and found they all had an acid content of 4.5% or higher, most quite a bit higher. It makes sense, because a company will dilute the product to a consistent acid percentage, all they have to do is add water.
So how much acidifier did I add? For the marinara, a little bit more than one TB of lemon juice per pint. For the salsa, 4 limes gave me 5 ounces of juice, or 10 TB for 7 pints, which works out to about 1.4 TB per pint. My salsa gets a lot of peppers. Over a pound of roasted sweet pepper was blended into the tomato base, and a pound of jalapenos were cut up and added, as well as a large onion, so a little extra acidifier can't hurt. I put the lemon or lime juice straight into the simmering pot. Citric acid is a crystalline solid and isn't going to boil off. Vinegar is another matter, the smell will tell you that the acetic acid is boiling off, so it should be added directly into the jars.
If you are interested in taking a deeper dive into the acidity question, I wrote a post several years ago that does that.
Finally, a general gripe about the canning recipes available. Most of the salsa recipes call for a processing time of 15 minutes for pints. The recipes for tomato sauce or marinara sauce that I've found in the Ball Blue Book and other places call for a processing time of 35 minutes for pints. Is there something I'm missing here? Because both are basically pureed tomatoes, without skins, that are hot-packed into the jars. One gets basil, the other gets peppers. Has anyone even thought about why a marinara needs to be boiled twice as long, or have the guidelines just become accepted doctrine? I processed both of them for 18 minutes.