One of the common problems with using "many" scripts is identifying which one is doing which rule...
The good news is that you can ask each script to echo to the screen as it runs.
I'd guess that there are three scripts, each echoing as "Phase x of 3"
Have a look inside the scripts you have found for text like that...
There is a good reason for using consecutive scripts like this, but if you want to be the master of them, you will need to discover what is really happening before you make any manual changes...
The
last script to run controls the rules...
So, if you have a script that starts by flushing and clearing the rulesets, it won't matter what comes before...
Have a look at this
iptables tutorial