Cool. One thing that I'm a bit concerned with is the on input event.
If you're going to echo the result anyways, wouldn't it be easier to make an alias for it, like /calc, instead of !calc in anywhere? It's just a suggestion.

Also, (though not very important in this script), you can combine these two parts:

    if (!$2) { msg # 4,1Please specify an equation. }
    else { msg # 4,1Math Problem by $nick :9 $2- 4. The Answer Is:9 $calc($2-)  }

by using an $iif.
This can be rewritten as:

msg # $+(4,1,$iif(!$2,Please specify an equation.,Math Problem by $nick :9 $2- 4. The Answer Is:9 $calc($2-) ))

Like I said, it's not necessary in this case, but it could save a lot of space in future scripts. Same thing goes for the on input event.