A. He doesn't need the latest version of F4SE, he needs the version that fits the game version.
D. Never delete mods from NMM unless you are sure those versions are still available on the Nexus, in case you want/need to go back to that older version of the mod. NMM deletes the mod from your PC without a possibility to recuperate it.
E. What lines are you talking about? I know that the custom.ini takes precedence over the Fallout4.ini, but it's the latter that needs the invalidateolderefiles and such lines added, but that's something that can be done from Bilago's Tweaker.
Ouf what a question, been a moment now so I'm not a 100% sure anymore but yea the 2 lines in custom.ini:
There's also an interface line to allow for a value/weight mod something like Strings=1
On the other hand I have noticed now that since the first edits, my .ini files are fat with lines that weren't there, I would wager in part because of bilago's tweaker and some other mods despite their esp's not being active. ;(