s/([a-z])\s+([a-z])/$1$2/g

Maybe you can have capital letters too, in which case you need to add a /i to that.

Another way that avoids capturing altogether: s/(?<=[a-z])\s+(?=[a-z])//g

Finally, I don't know how your current regex is working, but you can almost certainly do it in there rather than adding a new regex to first remove the whitespace. Something like this

$ perl -nle 'print "$1|$2" while /\s*([a-z\s]*[a-z])\s+(\d+)/g'
foo bar 1, baz qux 2, whatever 3, and some garbage.
foo bar|1
baz qux|2
whatever|3
[download]

perhaps?

-sauoq
"My two cents aren't worth a dime.";