Ok, the perl program is now correct... but your calling protocol is still junk.
I believe you're going to end up with a solution which is a convoluted mixture
of perl and "shell", or else do globbing inside the perl program, not unlike
what the OP did. Of course, it wouldn't be nearly so much of a problem on an
operating system with a Real Shell... ;-)
Technically correct if the OP's true intention was to replace only the first occurrence of each item in each line where it occurs. I tend to believe the OP probably wanted to replace all occurrences, not just one per line. I know you, jdporter (dmorgo bows) already know what character is missing ;-) but for the OP's benefit, adding a 'g' modifier would do the trick:
s/this/that/g; # substitutes this with that
s/one/two/g; # substitutes one with two