Customize!
You can edit which areas you want to run, optionally eliminating sections completely. Simply open up Act3LoadRandom.xml in a text editor, scroll down to the bottom of the file, and delete (or use XML comments) the appropriate line from the list below.
Code:
<TrinityLoadOnce questId="101758" stepId="1" >
<ProfileList>
<LoadProfileOnce profile="Skycrown.xml" />
<LoadProfileOnce profile="Stonefort.xml" />
<LoadProfileOnce profile="FoS-Rakkis.xml" />
<LoadProfileOnce profile="KeepDepths2.xml" />
<LoadProfileOnce profile="KeepDepths3.xml" />
<LoadProfileOnce profile="ArreatCrater1.xml" />
<LoadProfileOnce profile="ArreatCrater2.xml" />
<LoadProfileOnce profile="TowerDamned1-2.xml" />
<LoadProfileOnce profile="TowerCursed1-2.xml" />
<LoadProfileOnce profile="CoreOfArreat.xml" />
</ProfileList>
</TrinityLoadOnce>
For example, deleting the line <LoadProfileOnce profile="TowerDamned1-2.xml" /> will remove Tower of the Damned Levels 1 and 2 from the randomized profile selection.
So just delete <LoadProfileOnce profile="TowerDamned1-2.xml" /> and <LoadProfileOnce profile="TowerCursed1-2.xml" /> and they should not be ran.
If you want to run just the first level of whatever tower, that's more difficult since both levels are in the same file, you would need to edit the file and tweak a lot, or ask rixx to separate them in two files for you.