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for i in $(ls)

Using ls is superfluous, this is sufficient:
for i in *

sed 's/\/subject\/grin\*/\/subjects\/$i/g'

Try this:STR=$(strings MR* | grep MoCoseries)
Beware: you have to code for "What happens if the string is not found"

ls -S sorts by file size. The largest one comes first.

As for how I get it into $1 $2, try this:

set -- a b
echo $1
echo $2

I think I misunderstood. They're in 100 different directories, not in one pile, ergo they can be differentiated. Okay.

find /path/to/base -type d | while read LINE
do
set -- $(ls -S...