This code is actually already good.

Code:
on !*:JOIN:#:{
    set -e $+(%,ajwelcome.,$cid,#) $addtok($($+(%,ajwelcome.,$cid,#),2),$nick,44)
    if (!$timer($+(.ajw.,$cid,#))) { $+(.timer.ajw.,$cid,#) 1 3 ajwelcome # }
}
alias -l ajwelcome {
  if ($($+(%,ajwelcome.,$cid,$1),2)) {
    msg $1 welcome $v1 $+ , to my channel enjoy your nuggets!!.
    unset $+(%,ajwelcome.,$cid,$1)
  }
}


It did not work when you tried it because the original code do checking if your botname == your channelname. That can cause problem if your botname is not same with your channelname.

With this code, you can not turn on/off timer.
You have to modified nillen's code if your want able to turn on/off timer. But the + is the code already support multi network/connection and multi channel as you wanted it.