Ok, so with the headspace. The correct headspace for salsa is 1/2 inch. If you have had siphoning, use those first. They should be fine.
Personally, I still see no reason to not pressure can the recipe, but bump the time up to 35 min. in pressure canner. That would cover the peppers and onions, as long as you do not cook it longer than stated and make it too thick. Density is very important in salsa. They should be thin. Not thick like a store bought salsa. You can thicken it or drain off some of the liquid after canning.
The food at the top of the jars may darken. As long as they are still sealed and show no signs of spoilage, they should be fine. Next time you will be more careful with the pressure fluctations now that you know.
Don't increase the headspace.

Ever open a commercially made product packed in a jar. On its inside cover, you usually will find some of the product there not a 'crust', but nticably different. Its perfectly safe. If you ended up with an inch of headspace after canning, its probably the proper amount needed for filling jars. A half inch is usually for eight ounce jelly jars, but I would go slightly more for pints and even a bit more for quarts. There are slight differences in regular mouth quarts and wide mouth quarts.

Ken there is NO difference in pints than quarts for headspace. Not in the size nor the width of the sealing surface. Plus, salsa IS 1/2 inch, not an inch. Even one, the cranberry calls for only 1/4 inch. Where are you getting this stuff from ????
Read it here for yourself:

Here is a link that might be useful: Salsa recipes.

Thanks for the help on this! I feel confident now that we will not die from eating it now.

My salsa is thick, but I used tomatoes I had frozen and some that were fresh. I didn't have the 8 cups it called for, but I figured the frozen ones were kind of "mushed" down and it was probably equivalent to 8 cups. I do think I will use less of the paste however.

I think I will try this again this weekend, as I think I probably have enough ripe tomatoes to use fresh, instead of frozen.

Oh and one thing I learned.....Where gloves! Who knew 4 jalapenos would set your hands on fire like that! I knew enough to not rub my eyes, but never in the past have they done that to my skin. I guess I have only cut up one at a time before.

I go by Annie's recipe exactly...I mean I measure everything carefully and it is always thick...never has it not been thick. I also didn't know that it was recommended that we not Pressure can it any more...when did all that come about?

I just finished another load and it siphoned also. I thought I had everything down pat as far as timing and the gauge etc etc but I still had some siphoning....

Waving hand... add me to the list that didn't know Annie's Salsa was no longer PC approved, until a couple weeks ago, long after I had made two batches.

I also had siphoning on both batches, though much less so on the second batch since I brought the heat up slower, made sure there wasn't too much jiggling going on, and allowed it to cool way down before opening the PC. I did can for 35 minutes too, just to make sure.

Both batches are a *bit* on the thick side. I just started in on the first jar of the oldest batch tonight (canned about 7 weeks ago). If you don't see me around the next couple days, say a prayer for me. ;-)

PS It sure tastes good! :)

When a recipe calls for fresh tomatoes you are not supposed to use frozen or canned. Not unless the frozen ones were measured for a specific recipe and frozen in that amount. That is exactly why, it changes the density and the measurment will not be accurate.
Once the pressure is all the way down, after dropping naturally, you then remove the weight or counterweight. Then, set the timer for another 10 min. before you take the lid off and remove the jars. That helps with siphoning. This is a fairly new guideline.

I always pressure can my Salsa. I do not add the store bought tomato sauce or paste. I make my own sauce as I prefer a not so thick Salsa.

If the jars are syphoning out and leave more headspace when done, like over a half inch, it would make sense to increase the headspace slightly to prevent this in future batches. I doubt if anyone but you would use a ruler and measure the exact amount of head space in 'micro inches'. In many commercially canned glass jar products they have more than 1/2 inch of head space and I am not saying that an inch of headspace is needed, only that a half inch is the barest minimum, while I would not want a long term storage of a canned product to have more than an inch of headspace. I doubt if it would matter or even affect safety in any way if it were slightly over a half inch and up to an inch. But because you seem to go way overboard when working with canning specs sometime, I feel that we also have to get real here and go with what works best for us. You can quote and link to all the USDA sites and other points of interest, but some of those requirements are just silly and guessed at, and have not been thought out in a constructive manner. Scare tactics are taking some newbies to levels of doubt far beyond their comprehension. I bet there are a few who read all the horror sstories here and decide that its just to dangerous to do home canning, and give up.

Dare I mention a steam canner again, and all my personal testing involved, and how well it works for my specific canning? My no heat vacuum process has also been a great success for 3 years now with not a single bad jar of pickled pepperoncini yet.

Well, you do what you want, but trying to teach new people is important, and that they be taught correctly.
If making up your own things is what you want to do, fine.
I sure won't instruct people to do that, though. If you feel the facts are "guessed at", that is your choice. However, being in my position I truly don't believe they are "guessed" at.

The threads on the jars are meant for measuring, for those new to this. The first thread on a jar is 1/4 inch, the second down is 1/2 inch. The shoulder of the jar is 1 inch. That makes an easy way to determine headspace.
If the jars are siphoning there is reason for it happening, whether improper headspace or temperature fluctuation, too thick of a product, or removing too quickly from the canner.

Teaching and scaring are almost the same thing in many of the new posts. Being afraid of a pressure canner is the latest issue. I am not attempting to undermine you, only to point out that home canning is not an exact science and can be embellished on in many ways to make things safer to can. My sugarless jams for instance. They never spoil once opened. Its no big secret that if you have sufficient acid in a canned item its safty is much more pronounced. Just too accurate mesurements on the top of a Ball quart jar, wide mouth. Its first thread start measured 1/8 inch from the glass rim. The end of the single thread measured 7/16 inch from the rim. The glass bead to the rim measured 3/4 inch. Se for yourself! If your filling to the top of the treads, thats way too little at 1/8 inch, if your filling to the end of the thread, its still under 1/2 inch! There is only ONE single thread that surrounds the jar top and overlaps about 1 inch at its start and end.

Improper headspace must be quite common if I were to follow your advice to the letter..?

Syphoning can be caused by improper cooling as many have indicated in many recent posts.

Why would you use the threads on a jar to measure? I always measure from the inside of the rim to the contents. Some of the photos in the Blue book are stupid. Couldn't think of a better word. The page showing the head space for example. A photo of an empty jar would be better. The 1/4 measure is from the bottom of the beginning first thread and the 1/2 is measured from the bottom of the end thread. Seems this would be confusing to a newbie. Why not just measure with a ruler. Otherwise, you would need all your jars lined up perfectly to fill. I hold my jars when I fill them with liquids or jams.
Another is the photo of the basket of tomatoes being dipped in boiling water and still have the stem ends on. Only the expensive vine ripened tomatoes are sold this way. It would be impossible to pack large quantities of tomatoes with the stems left on. Holes would be poked in the neighboring tomatoes. Common sense rules.

The people who make the photos are not the same as the people who write the recipes and procedures. I hate it when they have TV commercials that depict perfectly colorful and neat looking foods and when you go there expecting that same thing in pictures, its a dissapointment. I measured the thread spacing from the centers of the glass threads. All of these can vary if you use a commercial product packed in glass jars that look similar to canning jars.

We teach using the threads because it is easy. This is an diagram of an empty jar to see how we instruct how to use the jar threads for headspace.
We don't have them use a ruler, takes too much time in my opinion.
Scare anyone ? I don't see anyone scaring anyone.