Here's a re-write using while loops. I'd also like to suggest that you see if there's a way to make those messages shorter, as the length of them might cause problems.
Code:
 if (%found) { 
  %i = 1
  while %i <= %found {
    if (%all == 6) { .msg $nick $C(1) $+ ( $+ $C(2) $+ overflow $+ $C(1) $+ ) $+ $C(1)  too many search results to display. }
    elseif ($findfile($r.srv(Fserve.1,Root.Dir),%search,%i)  {
    inc %current | .msg $nick $C(1) $+ ( $+ $C(2) $+  $+ %current $+  $+ $C(1) $+ ) file:( $+ $C(2) $+ $right($findfile($r.srv(Fserve.1,Root.Dir),%search,%i),$calc($len($findfile($r.srv(Fserve.1,Root.Dir),%search,%i)) - $len($r.srv(Fserve.1,Root.Dir)))) $+ $C(1) $+ )  size:( $+ $C(2) $+  $+ $big($findfile($r.srv(Fserve.1,Root.Dir),%search,%i)) $+  $+ $C(1) $+ ) trigger:( $+ $C(2) $+  $+ /ctcp $+ $chr(32) $+ $r.srv(Fserve.1,Trigger) $+  $+ $C(1) $+ )   }
    inc %i | inc %all
  }
}
if (%found.2) { 
  %i = 1
  while %i <= %found.2 {
    if (%all == 6) { .msg $nick $C(1) $+ ( $+ $C(2) $+ overflow $+ $C(1) $+ ) $+ $C(1)  too many search results to display. }
    elseif ($findfile($r.srv(Fserve.2,Root.Dir),%search,%i) != $null) { inc %current | .msg $nick $C(1) $+ ( $+ $C(2) $+  $+ %current $+  $+ $C(1) $+ ) file:( $+ $C(2) $+ $right($findfile($r.srv(Fserve.2,Root.Dir),%search,%i),$calc($len($findfile($r.srv(Fserve.2,Root.Dir),%search,%i)) - $len($r.srv(Fserve.2,Root.Dir)))) $+ $C(1) $+ )  size:( $+ $C(2) $+  $+ $big($findfile($r.srv(Fserve.2,Root.Dir),%search,%i)) $+  4+ $C(1) $+ )  trigger:( $+ $C(2) $+  $+ /ctcp $+ $chr(32) $+ $r.srv(Fserve.2,Trigger) $+  $+ $C(1) $+ ) }
  }
}
if (%found.3) { 
  %i = 1
  while (%i < %found.3) { 
    if (%all == 6) { .msg $nick $C(1) $+ ( $+ $C(2) $+ overflow $+ $C(1) $+ ) $+ $C(1)  too many search results to display. }
    elseif ($findfile($r.srv(Fserve.3,Root.Dir),%search,%i) != $null) { inc %current | .msg $nick $C(1) $+ ( $+ $C(2) $+  $+ %current $+  $+ $C(1) $+ ) file:( $+ $C(2) $+ $right($findfile($r.srv(Fserve.3,Root.Dir),%search,%i),$calc($len($findfile($r.srv(Fserve.3,Root.Dir),%search,%i)) - $len($r.srv(Fserve.3,Root.Dir)))) $+ $C(1) $+ )  size:( $+ $C(2) $+  $+ $big($findfile($r.srv(Fserve.3,Root.Dir),%search,%i)) $+  $+ $C(1) $+ )  trigger:( $+ $C(2) $+  $+ /ctcp $+ $chr(32) $+ $r.srv(Fserve.3,Trigger) $+  $+ $C(1) $+ ) }
    inc %i | inc %all
  }
}
if (%found.4) { 
  %i = 1
  while (%i < %found.4) { 
    if (%all == 6) { .msg $nick $C(1) $+ ( $+ $C(2) $+ overflow $+ $C(1) $+ ) $+ $C(1) too many search results to display. | halt }
    if ($findfile($r.srv(Fserve.4,Root.Dir),%search,%i) != $null) { inc %current | .msg $nick $C(1) $+ ( $+ $C(2) $+  $+ %current $+  $+ $C(1) $+ ) file:( $+ $C(2) $+ $right($findfile($r.srv(Fserve.4,Root.Dir),%search,%i),$calc($len($findfile($r.srv(Fserve.4,Root.Dir),search,%i)) - $len($r.srv(Fserve.4,Root.Dir)))) $+ $C(1) $+ )  size:( $+ $C(2) $+  $+ $big($findfile($r.srv(Fserve.4,Root.Dir),%search,%i)) $+  $+ $C(1) $+ )  trigger:( $+ $C(2) $+  $+ /ctcp $+ $chr(32) $+ $r.srv(Fserve.4,Trigger) $+  $+ $C(1) $+ ) }
    inc %i | inc %all
  }
}
if (%found.5) { 
  %i = 1
  while (%i < %found.5) { 
    if (%all == 6) { .msg $nick $C(1) $+ ( $+ $C(2) $+ overflow $+ $C(1) $+ ) $+ $C(1)  too many search results to display. | halt }
    if ($findfile($r.srv(Fserve.5,Root.Dir),%search,%i) != $null) { inc %current | .msg $nick $C(1) $+ ( $+ $C(2) $+  $+ %current $+  $+ $C(1) $+ ) file:( $+ $C(2) $+ $right($findfile($r.srv(Fserve.5,Root.Dir),%search,%i),$calc($len($findfile($r.srv(Fserve.5,Root.Dir),%search,%i)) - $len($r.srv(Fserve.5,Root.Dir)))) $+ $C(1) $+ )  size:( $+ $C(2) $+  $+ $big($findfile($r.srv(Fserve.5,Root.Dir),%search,%i)) $+  $+ $C(1) $+ )  trigger:(  $+ $C(2) $+  $+ /ctcp $+ $chr(32) $+ $r.srv(Fserve.5,Trigger) $+  $+ $C(1) $+ ) }
    inc %i | inc %all
  }
}