Have experienced some of these and offer some relief/insight to possible solutions. 
Basic
4. Phone causes lag using pip companion, use PyPipboy *found on Nexus and/or tablet or laptop, instead (if possible).
Fewer camera related issues with the following in fallout4Custom.ini (imperfect).

[Camera]
bApplyCameraNodeAnimations=0
fActorFadeOutBoundMax=0
fActorFadeOutLimit=0
fMinTimeInvisible=0
fOverShoulderOffsetCollisionScalar=0
fPitchZoomOutMaxDist=40
f1stHorzDampeningVelocityDampening=0.1
f1stHorzDampeningSpringConstant=0.0001
f1stVertDampeningVelocityDampening=0.1
f1stVertDampeningSpringConstant=0.0010
bDisableAutoVanityMode=1
fVanityModeMaxDist=2000.0000
fVertibirdAutoVanityZoom=350.0000
fVertibirdVanityModeMaxDist=2000.0000
fVertibirdVanityModeMinDist=350.0000
Settlements
5. Settlement values drop to zero randomly
Have noticed this, Especially with Sim Settlements, although staying in settlements for a time seems to "re-register" proper values... after a while.
Input 
1. Caps lock is a "stateless toggle". Game doesn't know which it was before (on or off) so whichever is opposite initial state is "run". Meaning one session could be off, another session on depending on how it started out.
Fallout4prefs.ini has bAlwaysRunByDefault=0/1 under [Controls]
2. Have experienced Tab not working to bring up Pip-Boy.
Happens to me After using workshop mode.
Enter and leave Workshop Mode again seems to fix it. (Took a while to discover that).
Graphical 
1b. blurry textures
Textures hold up better/longer (distance) with these settings in fallout4Custom.ini*
[General]
iTextureUpgradeDistance1=7500
iTextureUpgradeDistance0=7500
iTextureDegradeDistance1=7500
iTextureDegradeDistance0=7500
*not an absolute fix, but are 1:1 close up so don't look as good in near field.
Conversations 
2 & 3 Dropped words overlapping lines
Have experienced this, generally a caching/FPS issue. Reloading can help, crapload of utilities loaded to control caching/FPS seem to help once configured properly.
4 Dialogue wheel disappears
Happens often when not facing the Addressing NPC, or at a distance just between command/converse (can be confusing with turn-around weirdness). (Press Tab to make sure not in command mode). May have walked away from another conversation, possibly a while back... in which case, revert to previous save. Console command ~ GetPlayerWalkAwayFromDialogueScene may provide insight, but have yet to see that give useable feedback.
5. Default conversation for Piper not accessible
Piper is initiating an affinity forced dialogue/diatribe "always on good behavior", this Entire conversation MUST be completed to resume interacting with her, no matter how boring or ill timed it is. Also, other pending dialogues may be interfering, especially with multiple follower mods, or (un)certain quests.
Companion 
Death Bug
After much research this appears to be a result of full mobility damage to a companion's limb(s), which apparently cannot be restored by any known means (a flat-out bug). Only sound solution found so far is to revert to nearest previous save, if possible without saving current state.
Also: make sure fallout4prefs.ini in both %install%\fallout4\ folder and %user account%\games\fallout4\ are identical.
:whistling:Side note:
Have noticed with a lot of games/graphics upgrading and downgrading values by using BA2s, LODs, MipMaps, iTextureDegradeDistance0/1, sprites and such just needlessly complicate issues for competitive hardware by switching in and out back and forth instead of just straight up doing it once and for all. Sometimes loose files and no mipmaps is more acceptable, lighter weight, and less labor-intensive overall.