In today's climate it wouldn't be as easy as a couple of months ago.
I suppose I would look for a used, double-stack 9mm like a Glock 17, M&P9, XDM or SP2022 for the primary. Considering the budget, if it were a couple of months ago, the first pick would have been a <$400 Sp2022. Again, considering budget, the "backup gun" or EDC would probably be a single stack 9 from as small as a CM9/Nano which can be had for <$400 or maybe a LC9/SR9C/Shield if pocket carry and "BUG" wasn't a necessity.
So:
CM9/Nano and SP2022. Considering budget and climate, you might squeak by.
However, this part confuses my simple, reptilian brain
My "already EDC?" You mean I can pick two guns along with one I already EDC? If so, then the choices change.
If you mean the "self defense/home defense pistol" is intended to be an EDC simultaneously, then that also changes the selection.
If the big gun is to be an EDC, then it just got smaller. Glock 19 or one of the somewhat smaller "compact" double stack nines.
If the small gun is really a BUG and both are intended for EDC, then the selection for my criteria means it must be pocket (holster) carried. Definitely no bigger than the CM9/Nano (or P290, which was my choice of the three.)
ETA: You gonna EDC that 17/19 with the light or does the light only go onto the gun when it goes into the bedside safe? If EDC, than I would strongly consider a good, separate torch or not try carrying an integrated light on the pistol. My bedside Glock 17 has an attached light but there is also a good torch in that same bedside vault.
You can either have $1000 for a backup if your EDC is already good enough and meets your criteria for EDC, or you can have $1000 for a backup and a new EDC. Basically, you have $1000 to add to what you already have. You have to either pick a backup for your EDC, or a backup and a new EDC. Not looking for me, just curious to what everyone's tastes are.
As for the flashlight comment. I already carry a small flashlight and a penlight everyday, so a rail mounted light is my next step. I keep my penlight in my work jacket and I keep the other flashlight on my nightstand at night and in my pocket once I get dressed.