I know Macs are based on BSD so I am asking this question here.

I have 2 sets of machines. First set is the obvious windows PCs and the other is Macs. What we do on the windows units, dump a ghost image onto the machine and then use a series of batch files to move files, set users and to join the active directory. On the Macs we do everything by hand and it takes a LONG time to do alot of them at once.

What I want to know is how do how to get the Macs (BSD) to run a file, such as bash or perl, to update the OS and add to Active directory without having to log into the mac? So after the image is dumped onto the machine, it should run:

/usr/local/bin/ktcheck -c sha1 -h <server>

/usr/local/bin/fsdiff -A -c sha1 /|/usr/local/bin/lapply -h <server>

and then Join it to the active directory. Using a master script. And the other question would be on the second one (which takes about 2 hours) how to show progress if the first question is capable.

How do I go about accomplishing these two?

If you know the command line commands you can use cron.

To make commands depend on the successful completion of a previous job you just concatenate the jobs like so "job1&&job2&&...&&jobn".

<inadvertent double post deleted>

this will allow to run once then delete the job so it does not run again? I only want the script to run at setup.

Depends from how you set up cron. I (mis?)-understood that you want to do this periodically. Else you simply issue the concatenated jobs from the command line. But maybe I just didn't get what you really want to do...

basically I want when the machine restarts the first time, it will run 2 commands on its on and join AD without ever having anyone entering in the command. It will do it once and that is it.

Sure. Use cron with the @reboot option.
http://linux.die.net/man/5/crontab