how to merge two files consistently line by line

This Perl one-liner will display the necessary renames:

perl -e 'open $f[$_-1], "file$_.txt" for 1,2; print "rename @n\n" while chomp(@n = map ''.<$_>, @f)'

If this works for you then replace the print statement with a real rename and use

perl -e 'open $f[$_-1], "file$_.txt" for 1,2; rename @n while chomp(@n = map ''.<$_>, @f)'

to do the actual renaming.

You can use paste to format the files side by side:

$ paste -d" " file1.txt file2.txt
/etc/port1-192.9.200.1-255.555.255.0 /etc/port1-192.90.2.1-255.555.0.0
/etc/port2-192.9.200.1-255.555.255.0 /etc/port2-192.90.2.1-255.555.0.0
/etc/port3-192.9.200.1-255.555.255.0 /etc/port3-192.90.2.1-255.555.0.0
/etc/port4-192.9.200.1-255.555.255.0 /etc/port4-192.90.2.1-255.555.0.0
/etc/port5-192.9.200.1-255.555.255.0 /etc/port5-192.90.2.1-255.555.0.0

E.g.:

$ paste -d" " file1.txt file2.txt | while read from to; do echo mv "${from}" "${to}"; done
mv /etc/port1-192.9.200.1-255.555.255.0 /etc/port1-192.90.2.1-255.555.0.0
mv /etc/port2-192.9.200.1-255.555.255.0 /etc/port2-192.90.2.1-255.555.0.0
mv /etc/port3-192.9.200.1-255.555.255.0 /etc/port3-192.90.2.1-255.555.0.0
mv /etc/port4-192.9.200.1-255.555.255.0 /etc/port4-192.90.2.1-255.555.0.0
mv /etc/port5-192.9.200.1-255.555.255.0 /etc/port5-192.90.2.1-255.555.0.0

Of course you would want to throw in some safety checks ([ -f "${from}" ], ...).

Disclaimer: Works only if there are no spaces in your filenames.

paste -d " " file1.txt file2.txt

works great for this job.

But in case you are handling text files in a Windows environment and make use of GNU paste, make sure to transform the files to Unix format (CR) and do not use files with (CR-LF).

GNU paste does not seem to handle DOS formats properly and parsing is unpredictable. The expected output is erratic and unexpected without warnings.

You may use gVim to transform them easily (menu Edit → File Settings → File Format).