#!/usr/bin/perl -w
use strict;

my $line;

while ($line = <DATA>)
{
   if ($line =~ m/\s*while/)
   {
      process_while();
      next;
   }
   print $line;
}

sub process_while
{
   #tweaked to allow the "(" after "while" to be on next line 
   #or have blank lines before the "("
   #that's for this for loop does find the first "(" line
   
   for ( ;$line !~ /\(/;(print $line),$line=(<DATA>)){}

   for (my $n_cndx =1; $line !~ m/\{/ ; $line=(<DATA>) )              
   {
      $line =~ s/(\w+)(\s*)(&&|\|\||\s*\)|\s*\n)/ $n_cndx++." $1$2$3" /ge;
      
      print $line;
   } 
}
=Prints:
 while 
 (
          (  
             1 condition1 && 
             2 condition2 && 
             3 condition3 
          ) 
      || 
          ( 
             4 condition4 || 
             5 condition5 && 
             6 condition6 
           ) 
 )
{more statements};
while(1 X){}
=cut

__DATA__
while 
(
         (  
            condition1 && 
            condition2 && 
            condition3 
         ) 
     || 
         ( 
            condition4 || 
            condition5 && 
            condition6 
          ) 
)
{more statements};
while(X){}