This really depends on what you have as an input and want to output, and what rules you apply to do it .
I'm afraid the rules you have given do not create the output you want since $a[0] appears unmodified in the output.

To do what something approaching what you asked, i used an array of array . It takes your @a and applies these rules :

if $a[0] has rowspan=2 then we have to place one empty <th></th> in th
+e corresponding place of $a[1]
if rowspan=3 the we have to place empty <th></th> in $a[1] and $a[2] i
+n corresponding place.
[download]

I understand "corresponding place" as "at the begining of the same element number but in the other arrays" .

#!perl ;
use strict ;
use warnings ;

my @a ;
my @b ;
my @c ; 
my @splitted ;
my $i ;
my $j ; 
my $aref ;

$a[0] = "<th><rowspan=2>Target protein</th><th><colspan=2>Purified pro
+tein concentration</th><th><rowspan=3>Activity</th>" ;
$a[1] = "<th>Mg/liter culture</th><th>Mg/g dry cell weight</th>" ;
$a[2] = "<th>Mg/liter culture</th><th>Mg/g dry cell weight</th>" ;

# First build an array of array

foreach $i (0..$#a) {

    @splitted  =  $a[$i] =~ m#(<th>.*?</th>)#g   ; 
    $b[$i][$_] = shift @splitted  for  (0..$#splitted )  
    
}

# Apply rules

$aref = $b[0];

for $j ( 0 .. $#{$aref}  ) {

    if  ( $b[0][$j] =~ m/rowspan=(\d)/  &&  $1 == 2 ) {     
    
        $b[1][$j] = "<th></th>" . $b[1][$j]  ;
    
    }
    
    elsif ( $b[0][$j] =~ m/rowspan=(\d)/  &&  $1 == 3 ) {     
    
        $b[1][$j] = "<th></th>" . $b[1][$j] ;    
        $b[2][$j] = "<th></th>" . $b[2][$j]  ;    
    }
    
}

# Merge into a simple array

for $i ( 0 .. $#b) {
      
    $aref = $b[$i];
        
    $c[$i] = join "", @$aref ;
    
}
    
# Format and print result 

 foreach (@c) {$_ =~ s#</th>#</th>\n#g;   print $_, "\n\n" ;  }
[download]

This will output (with some warnings ):

<th><rowspan=2>Target protein</th>
<th><colspan=2>Purified protein concentration</th>
<th><rowspan=3>Activity</th>

<th></th>
<th>Mg/liter culture</th>
<th>Mg/g dry cell weight</th>
<th></th>

<th>Mg/liter culture</th>
<th>Mg/g dry cell weight</th>
<th></th>
[download]

So if you play around with Array of Array you might get to something matching exactly your needs .

Hope this helps,

zlr _