How would I go about writing a simple code to be on a timer, where it runs an alias to join a channel from a list, executes another alias, then parts the channel, then waits a couple of mins and joins the next channel on the list, and so on.

timer1 0 300 timeralias

timeralias {
...channel list here pick the first channel from the list...
join channel
...execute called alias...
...wait 5 mins...
...exceute the timeralias agian to pick the next channel and so on...
}

What I'm trying to do is join a list of channels, 1 at a time, execute my who-alias, which executes my trace-alias, which traces each user on the current channel, wait 3-5 mins for all the traces to finish on the current channel and then move to the next channel on the list. Once the who-alias is executed, the script can immediately leave the current channel and just wait for the traces to finish, before it joins the next channel on the list.

You need to work with events here, and you won't be needing timers at all, unless the reason you want to use them is not specifically to avoid a flood disconnection.

I need to know what your "trace-alias" does, in order to know which event to wait for before "tracing" the following nickname. I just hope it doesn't involve some sort of port scan on the user. If it involves knowing which channels a user is on by running a WHOIS on each one of them, then you could even save running the WHO command, unless you need to fill your IAL right after joining.