a) Welcome to Perl, and welcome to the monastery.
b) The monks aren't here to do your work for you. Don't just drop a ton of code on us and expect us to make it work.
c) Not all Perl programs are this nasty. That's how we wrote them 30 years ago. (Almost! Perl is 30 in December.)
d) ETXLinkID,TranscomLinkID,TranscomLen,TranscomLenFrac,EtxLenFrac,EtxLen seems to be what the program outputs right now, correct? So you don't need to calculate any new results, you just need to add a header line to the output?
e) All the output appears to happen in the final foreach loop. If you need to print a header before the other output, print it right before that.