Your regular expression: $line =~ s/ s{2,}/\t/s is converting " ss" and " ssss" to tabs and it is only converting the first one because you don't have a global flag at the end. To replace the tabs you would need s/\s\s+/\t/g or s/\s{2,}/\t/g. Note the backslash before the "s".

As for keeping the final newline, I would recommend stripping it before you apply the regex and adding it after you are done. There are ways to do that with regular expressions alone but your regular expression would be quite complicated. So the code to prep the line should look something like this:

while(my $line = <FH>) {
   #strip newline
   chomp $line;

   #replace runs of two or more spaces with tabs
   $line =~ s/\s\s+/\t/g;

   #add back newline
   $line .= "\n";

   #.... do whatever with $line ....
}
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Best, beth