This code is of course not going to parse some arbitrary C code "while" statement lines(s)! It does appear to execute your test case as presented and I hope a starting point for you for further refinement. Of course this Perl code assumes that you have at least compilable C code.

Curiosity gets the better of me and I'm wondering what the application is? If it is some kind of code complexity measurement, perhaps the number of && and || operators would be more to what you want?

UPDATE: Made some small revisions to previous code. After seeing your post with an example and desired output.

#!/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){}
[download]

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

my $line;

while ($line = <DATA>)
{
   if ($line =~ m/while\s*\(/) #perhaps m/^\s*while/ ? 
                               #think about "while in a comment". 
                               #other border cases...
   {
      process_while();
      next;
   }
   print $line;
}

sub process_while
{
   my $i =1;
   while (1)   #normally while(1) not a good idea, but
               #I figure its ok here.
   {
      $line =~ s/(\w+)(\s*)(&&|\|\||\s*\))/ $i++." $1$2$3" /ge;
      print $line;
      return if $line =~ m/{/;
      $line = (<DATA>);
   } 
}

=Prints:
 some statement;
 while( ( 1 condition1 && 2 condition2 && 3 condition3 ) || 
 ( 4 condition4 || 5 condition5 && 6 condition6 ) { #statements; }
 while( ( 1 condition1 ) || 
 ( 2 condition2 || 3 condition3 && 4 condition4 ) { #statements; }
 while(  1 condition1 &&  2 condition2 ||  3 condition3 ) 
 { #statements; }
 more statements;
=cut

__DATA__
some statement;
while( ( condition1 && condition2 && condition3 ) || 
( condition4 || condition5 && condition6 ) { #statements; }
while( ( condition1 ) || 
( condition2 || condition3 && condition4 ) { #statements; }
while(  condition1 &&  condition2 ||  condition3 ) 
{ #statements; }
more statements;
[download]