Just wanted to share the result of my experience, after 4 months, since somebody may come across this page.
The reason for the stutter and many other problems in Adobe Premiere was the K-Lite Codec Pack. It was hard to find out, although its been written on many forums. So never install it and its not enough to simply uninstall it, I had to format.
Unfortunately there’s not a solution like I’ve asked. I had to make many new sequences and sometimes export – imports.