Bash script - iterate through folders and move into folders of 1000 - linux

Question

I have 1.2 million files split out into folders, like so:
Everything
..........Folder 1
..................File 1
..................File 2
..................File 3
..................File 4
..................File 5 etc
..........Folder 2
..................File 1
..................File 2
..................File 3
..................File 4
..................File 5 etc
If I cd into Folder 1 I can run the following script to organize the files there into folders called 1, 2, 3, etc. of 1000 files each:
dir="${1-.}"
x="${2-1000}"
let n=0
let sub=0
while IFS= read -r file ; do
if [ $(bc <<< "$n % $x") -eq 0 ] ; then
let sub+=1
mkdir -p "$sub"
n=0
fi
mv "$file" "$sub"
let n+=1
done < <(find "$dir" -maxdepth 1 -type f)
However I really would like to run it once on the Everything folder at the top level. From there it would consider the child folders, and do the by-1000 sorting so I could move everything out of Folder 1, Folder 2, etc. and into folders of 1000 items each called 1, 2, 3, etc.
Any ideas?
Edit: Heres how I would like the files to end up (as per comments):
Everything
..........Folder1
.................file1(these filenames can be anything, they shouldnt be renamed)
.................(every file in between so file2 > file 999)
.................file1000
..........Folder2
.................file1001
.................(every file in between so file1002 > file file1999)
.................file2000
Every single possible file that is in the original folder structure is grouped into folders of 1000 items under the top level.

Answer 1

Let's assume your script is called organize.sh, and the Everything folder contains only directories. Try the following:
cd Everything
for d in *; do
pushd $d
bash ~/temp/organize.sh
popd
done
Update
To answer Tom's question in the comment: you only need one copy of organize.sh. Say if you put it in ~/temp, then you can invoke as updated above.

Answer 2

Pseudo Algo:
1) Do ls for all your directories and store them in a file.
2) Do cd into each directory you copied into your file.
3) Sort all your files
4) Do cd ..
5) Repeat step 2-4 in a for loop.