"3999 affected the database. The database in Swann's proposal is implied to be literally its tool for deciding all of reality and existence; from beings such as the All-Mighty to smaller entities like 058. (And it is also called the plot itself)"
This is super super wrong. The database isn't the tool for deciding reality and existence, Swann can change existence outside of it. The All-Mighty doesn't have an entry in the database, he could not be affected by Swann if what you were saying is true.
Affecting the database is just data manipulation. Foundation researchers do it, and many other harmless SCPs change articles into garbage without messing up reality.
ALSO, there are specific parts of the SCP database that do translate into effects on reality, according to Kate McTiriss' proposal this is slot SCP-001, but we have no way of telling if this proposal is true in 3999's canon, nor can we tell if 3999 can effect that slot specifically, nor can we tell if 3999 knows about that slot.
The database can also affect reality through 3309, where badly-written articles put in by researchers get deleted from the database as well as reality, but 3999 has never demonstrated knowledge or use of this ever.
I don't know where you got it being called "the plot itself" but that's a really weird statement, modifying the database =/= modifying the plot, but when Swann makes changes to reality the database is modified too to keep it consistent.
"Not only this Monika still has a human mind, emotions, (she literally resisted a re-integration into reality because she didnt want the player to make her sad again) etc. and even with all of her powers she'd still go completely ******* insane facing 3999."
3999 doesn't have madness manip.
"and we have to realize that 3999 was making a Level 3 Foundation Personnel go bloody insane"
Level 3 foundation personnel don't have special resistance to mind manip. In fact, that personnel was driven insane because they were tortured for millions of years, and the only reason they couldn't break out is because they're not a ******* universal reality warper like Monika is.
"The Foundation has NEVER given up even when faced with the scarlet king screaming bloody murder and wanting them dead or the sun itself melting them all to ashes and amalgamating them into monstrosities.. And 3999 made him go numb with insanity for 3 million years until he figured it all out."
The Foundation has just given up over certain things, and resigned to not telling their researchers that they'd given up. I believe this was over some eldritch horror being like the Scarlet King actually. And the sun melting them didn't happen over a few million years, and a lot of them would have given up, sure.
"also all his hax to go with it "
I've already explained why his hax wouldn't be enough.
"its as if 3999 might have reduced existence to nothingness and then turned it into a living visual nightmare for talloran just to spite him!"
This is literally just conjecture.
"Plus Monika starting with erasure does jack shit on abstract existence"
Monika doesn't start with existence erasure. She starts with plot manip and mind manip, which 3999 doesn't have a resistance to.
If you're going to wank SCP so hard at least put it towards something like upgrading it to 1-A.