Ok, which bit controls how it displays..

window -ls @chanlist 10 100 788 200

tells mIRC to make a custom window 10 pixels from the left, 100 pixels down,
788 pixels wide and 200 pixels high

window -ls @chanlist 10 100 788 200
tells mIRC to sort the window



"aline @chanlist $right(... $+ $3,4) $2 $4-"

this adds a line to the window every time the server sends data

RAW data is prefixed and the prefix is in $1 which you dont need or want
$2 is the channel name
$3 is the number of users in the channel
$4 to $whatever will be the topic for that channel

in order to get the window to sort by the number of users in the channels
the order you want is $3 $2 $4-


also it still grabs focus for mIRC as a program every time it refreshes
this might be a version issue, what version of mIRC are you using?