Answers to your questions:
1. No idea on this, I have not experienced this before
2. Okay, it's changed in the manuals for the next time they are uploaded
3. If I can remember correctly, sometimes is takes a sim restart for the smoke effects to turn off. I've always flown with them off (for the same reason on the ground).
4. The SimObjects directory is the back-up location of the manuals, since people are bound to be in there is adding a livery. The main location of the manuals should be in Prepar3D main/ecosystem/Aerosoft, additionally there should be a shortcut to the manuals in the Windows start menu under "Aerosoft F-14" along with the link to the IP config for shared cockpit. From what I understand the ecosystem directory is the common location for all Aerosoft's manuals in Prepar3Dv4.
Do you have the valve steam client running in the Windows tray or the windows firewall disabled? Both have negative site effects on the font installation which could explain what you witnessed. That's why I asked you to re-install.