Re multi-line output, the code you show has you adding a newline to your data at line 4 as well as in the output lines -- the ones pointed out by johngg. And choroba is right about the regex, though I'd use "precise" rather than "firm."

But the code you show has very little to do with the output you claim or that you say you want as the vars $port, $speed and $link are neither instantiated nor assigned a value.

Downvoted, for abusing the Monastery's goodwill.

Update: Thanks jethro for msg which made me realize I'd misread the "=" in lines 8, 9 and 10 as an attempt at assignment. It isn't of course; it's merely redundant since the text includes the verb "is." However....

OP's position counts are for the header rather than the actual data... and the inclusion of commented lines that bear no relevance to the problem simply wastes the Monks' time.

#!/usr/bin/perl
use 5.014;
# 990400

# all global; too lazy to work hard on OP's code
my ($line, $ind, $port, $speed, $link);


while (<DATA>) {

    $line = $_;
    if ( $line =~ /\bup\b/ ) {
        print "port is ", $port, substr($line,1,2). ", ";
        print "speed is ", $speed, substr($line,7,5). ", ";
        print "link is ", $link, substr($line,42,4)."\n";
    }
}

# NB Port 10 Link status changed to "up" (and indented as in Port 19)

__DATA__
------------------------------------------------------------------
Port   Speed    Duplex     Flow Ctrl      Link       Name
----   -----   --------  --TX-----RX--   ------     ------
  1    10000     full      no     no      down      1       
  2    10000     full      no     no      down      2       
  3    10000     full      no     no      down      3       
  4    10000     full      no     no      down      4       
  5    10000     full      no     no      down      5       
  6    10000     full      no     no      down      6       
  7    10000     full      no     no      down      7       
  8    10000     full      no     no      down      8       
  9    10000     full      no     no      down      9       
 10    10000     full      no     no       up       10      
 11    10000     full      no     no      down      11      
 12    10000     full      no     no      down      12      
 13    10000     full      no     no      down      13      
 14    10000     full      no     no      down      14      
 15    10000     full      no     no      down      15      
 16    10000     full      no     no      down      16      
 17    1G/10G    full      no     no      down      17      
 18    1G/10G    full      no     no      down      18      
 19     1000     full      no     no       up       19      
 20    10000     full      no     no      down      20
[download]

Output:

C:\> 990400.pl
port is 10, speed is 10000, link is up
port is 19, speed is  1000, link is  up
[download]