I'm sorry, I don't understand the $fh_in and $fh_out variables.

You used global vars GPXDATA and MYFILE. I switched to using lexical vars with more meaningful names: $fh_in and $fh_out. ("fh" stands for "file handle".)

If someone could give me a more detailed reply on how to read and merge all lines following the 2 first lines, in all .ktf files in a directory, and write it to a file, I would be eternally grateful! :)

I don't know how we can get more detailed then providing the code that does that.