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Sauce Simmer Fail

Posting more to be informative and get comments on simmering and other's results with simmering of a sauce.  
 
Yesterday started the milling of 6KG of chilies that have been in a salt ferment for 30 days.  
 
Basic recipe proportions and ingredients are: (using a previous batch as an example)
THAI CHILI 3390 GMS BEFORE SMOKING, 2720 after
9 HEADS OF GARLIC  298 GMS BEFORE, 272 GMS AFTER
24 SHALLOTS 136 GMS BEFORE, 130 GMS AFTER
TOTAL WEIGHT AFTER 3120 GMS
SALT 106 GMS
4 CUPS WATER
 
I went straight from the fermenting bottles to the food mill.  As I will illustrate later, I found this was a mistake and it would not maintain the sauce consistency I've always gotten straining through a screen.
 
After milling, I noticed that the sauce was watery, i.e. tabasco consistency.  I figured OK lets do a simmer of the sauce and that will thicken it up.  I had bad results previously boiling thai chili sauce with oily looking globules at the top of my bottles once bottled.  That discussion is here.  
I also wanted to simmer to insure the cessation of fermentation on top of the addition of vinegar.
 
To the 4 liters of watery sauce, I added 1 liter of pineapple vinegar.  Then I began the simmering.  I took temperature readings and never went above 160°F.  As the sauce was simmering, it began to separate AGAIN!  I simmered the sauce (stainless steel Calphalon pot) for less than an hour as watching the dark red substance separating from the sauce just really pissed me off.  I did my best to skim a lot of the red floating material.  This is the same effed up mess I got after boiling the sauce previously....except it was watery.
 
At this point I have a watery freakin sauce and crap floating all over looking like %$#%$.  I then realized I had skipped a step that I usually do which is to take the fermented mash and then run it through the blender for one minute to REALLY make it fine.  I would then mill it thru a screen like so.
 
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This is new sauce on the left, old preferred thick sauce style on the right
 
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Here is the separated sauce in the pot.  Nasty looking.  
 
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Close up of the separation.   Fugly mess!
 
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So with my watery funky looking sauce, I decide, since I still have most of the chili chaff that had been milled out by the food mill, I would throw that back into the NOW vinegared sauce and put it all through the blender.  Something I should have done before putting it all through the food mill.  <face palm>
 
Now that it has been re-blended and run through the food mill again with the smaller holed screen this time, the sauce is now thick a la sriracha sauce and how I want it to be.  I will not simmer this again as it is now completely (thankfully) homogenous even after sitting for an hour.  I really don't have good luck with heat and this recipe/chili!!!
With a pH of 2.8 this sauce should be fine in sterilized bottles.
 
The reason I didn't use the blender coming from the fermenting bottles as I usually do is that I was excited, in a way, to be using the food mill for the first time.  So I jumped the gun as it were and jumped right to the milling step and a watery sauce is what I ended up with!
 
  
 
 
 
Just finished bottling and the sauce is a really nice red color with no ugliness as illustrated above.  I found during the beginning of the bottling that the seeds were not completely removed by the food mill since I didn't strain through the screen.  This leaves very fine seed particles in the sauce which I decided was OK this time.  It's an "artisan" sauce so I think this gives me some artistic license to vary things a bit.  Straining though the screen after the milling would eliminate this "issue".
 
It was good to get 23 -180ml bottles and 10 - 60ml bottles completed after the near disaster.
 
 
 
Here is a good visual reference of my boiled sauce vs the present simmered sauce that I was able to rescue.  
This new batch is visually beautiful with a bright red color & homogenous appearance.  Compare that to a boiled batch next to it on the left!  I'm really happy I was able to save this batch.  You can see the flecks of seeds that made it through the food mill, & the plate I used is behind the bottles.
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The 2nd photo is pretty gross looking, but I kept the bowl of sauce (long enough for a photo) that I skimmed off the top while simmering the present batch.  I tossed that.  
 
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