hi

u use if $me isin %var

if your nick is "bam" and we type bamboo u will hightlight??? dont use isin here use $findtok is better

if (%hiservers == on) { aline @highlight 7 $+ $server $nick 14highlighted you at 7 $+ $time 14in 7 $+ $chan  }
if (%hiservers == off) { aline @highlight 7 $+        $nick 14highlighted you at 7 $+ $time 14in 7 $+ $chan  }

u can replace it by

aline @highlight 7 $+ $iif(%hiservers == on,$server) $nick 14highlighted you at 7 $+ $time 14in 7 $+ # 

and u can replace aline by echo i u want

why u put /window -e u dont need edit box no?!!

"if (%highlights == off) { halt }" is unless u can remove it

so u can do this

on *:text:*:#:{
  tokenize 32 $strip($1-)
  if (%highlights == on) {
    if $findtok($1-,$me,32) {
      if ($2 == $null) && (%hrep == on) {
        msg # $nick $+ ?
        aline @highlight 0....14Replied? 7y
      }
      aline @highlight 7 $+ $iif(%hiservers == on,$server) $nick 14highlighted you at 7 $+ $time 14in 7 $+ # 
      aline @highlight 0..14With message: 7 $+ $iif($2,$1-,No message) 
    }
  }
}

for alias highlights & alias hrep u can do it like this

alias hrep if ($istok(on.off,$1,46)) set %hrep $1

alias highlights {
  if ($istok(on.off,$1,46)) {
    set %highlights $1
    window $iif($1 == on,-enxz,-c) @highlight
  }
  elseif ($1 == clear) dline @highlight 1- $+ $line(@highlight,0)
  elseif (($1 == servers) && ($istok(on.off,$2,46))) set %hiservers $2
}

better use 1 & 0 for variable then u'll use it like this

if (%var) <==== if %var = 1 the commande will be execute if %var = 0 it's dont

so finaly your code can be like this

on *:LOAD:{
  echo -a Highlight script by sloth loaded.
  echo -a To turn it on /highlights on
  echo -a To turn it off /highlights off
  echo -a To clear highlight log /highlights clear
  echo -a To set automatic replies on or off
  echo -a use /hrep on or /hrep off
  echo -a Use /highlights servers on to enable multi-server logging
  echo -a Use /highlights servers off to disable multi-server logging
  echo -a version 0.4
  set %highlights 1
  set %hrep 0
  set %hiservers 0
}
on *:text:*:#:{
  tokenize 32 $strip($1-)
  if (%highlights) {
    if $findtok($1-,$me,32) {
      if ($2 == $null) && (%hrep) {
        msg # $nick $+ ?
        aline @highlight 0....14Replied? 7y
      }
      aline @highlight 7 $+ $iif(%hiservers,$server) $nick 14highlighted you at 7 $+ $time 14in 7 $+ # 
      aline @highlight 0..14With message: 7 $+ $iif($2,$1-,No message) 
    }
  }
}
alias hrep if ($istok(on.off,$1,46)) set %hrep $iif($1 == on,1)
alias highlights {
  if ($istok(on.off,$1,46)) {
    set %highlights $iif($1 == on,1)
    window $iif($1 == on,-enxz,-c) @highlight
  }
  elseif ($1 == clear) dline @highlight 1- $+ $line(@highlight,0)
  elseif (($1 == servers) && ($istok(on.off,$2,46))) set %hiservers $iif($2 == on,1)
}