@kinggath
I have not seen the slow saves with my SSD to the magnitude as I started a new game with the latest version of SS2/chapter 2. I am just about ready to power up the beacon to call Jake.
But beyond this, there are a couple other issues I have found and have worked to resolve that may lead to another finger of "truth" in this hunt and to help others...
Survival and autosaves - downloaded Ultimate Survival Mode to enable auto saves so I could disable the autosave after sleeping/resting.
Random crashes - downloaded High FPS Fix and Weapon Debris - considerable improvement and not seen a similar crash
Crashing - when entering into pip-boy (that issue with SS1 long ago... there was a sorting tagging mod that was using up what RAM it needed and crashed)
Long loading times (starting the game) - this occasionally happens, and the next time, it is fast.
Save and exit to desktop - total freeze and can't even using ctrl alt delete - hard reboot of computer (alienware) - haven't had this type of issue in forever.
Exiting game - exit to menu and then exit game instead of desktop is quick and no lockups.
A new mod version of Better Settlement Defence using which I didn't individually test independant of SS2/Chapter 2 - it is workshop framework / F4SE dependant.
My 2 pennies at this time is somewhere in the WSFW and F4SE....
John
PS - I could try this file as perfect spot to do so, but with my SSD I don't really have long save issues.... 15-20 seconds is considerably longer than mostly instant.