Synthetic Stucco - Dryvit - Repair - How

I bought my home a little over 7 years ago and it is sheathed with a Dryvit type synthetic stucco material. This was all before the horror stories of moisture getting behind the stuff and rotting things.
Nevetheless, I have one of these home in the Chicago area and while we do not have high humidity like the south I was never too worried since everything looked good, to me.
Well, we had the house inspected and found that around a number of windows the moisture readings were behind the synthetic material were nearly 30%, but nothing spongey was found. It would appear that moisture enters through the mitered joints of the window and gets behind the synthetic material.
I also added a deck a few years ago and did not cut into the synthetic material to add a drip edge. I decide to drill through the material and flood the hole and bolt with GE silicon. I then added copious amounts of GE Silicon to the wall where the ledger board went. Still, I got a high reading under the deck below the ledger board. I still cannot believe moisture entered from the bolt penetrations.
Because I plan to sell my house I will now hire a contractor to replace all window caulking, and make all the other repairs and then get the complete installation warranted. I expect the repairs to run me $10k-$15K, and a one year warranty to be $1.5K.
Anyone else got a similar story, experience, or advice.
Thanks, John
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