Hi sectopod! First of all, the milestone version is terribly out of date for most of the mods, so unfortunately most of what you did to install it will not help you with installing Piratez. It did install all the necessary libraries for the newer versions of the executable, so that will be helpful going forward.
To install Piratez on Ubuntu, you'll need to download the .zip package from
Dioxine's thread, and choose a place to unpack it that is *not* the same directory as any of the OpenXcom 1.0 stuff. For example, you can just unpack it in your Downloads folder and leave it as a separate installation from the milestone. Next, you'll need the new executable from
Meridian's thread. There's a link there to a directory of various builds for linux, just find the one that matches Ubuntu 14.04 (Trusty Tahr) and your architecture (32 or 64 bit). Download the zip archive from there, and copy the OpenXcomEx file into the Piratez folder. Then, copy the data from the original game into the UFO subfolder of the Piratez directory. You should be able to run OpenXcomEx either from command line cd'd into that directory or by just double-clicking.
Edit:
For any other mods, I'd seriously suggest either just ignoring the original OpenXcom you installed or removing it from your system - it has a different directory structure for installing mods than the latest versions, and you will confuse yourself trying to keep those straight. For installing future mods, you should be able to unpack them in the [path/to/new/openxcom/install]/user/mods folder and be able to run them from there. For example, I use Meridian's OpenXcom Extended Plus executable to run a number of different mods based on shell scripts. My openxcom directory looks like this:
common
config_piratez # contains options.cfg file for running Piratez
config_xcomfiles # contains options.cfg file for running XComFiles
config_ufo # contains options.cfg for running the game with no mods
config_tftd # contains options.cfg for running TFTD
standard
TFTD
UFO
user
-> mods
-> Piratez
-> XComFiles
-> Any other mods I want to use
OpenXcomEx # The executable file to run the game
piratez.sh # Shell script that runs OpenXcomEx with config_piratez
files.sh # Shell script that runs OpenXcomEx with config_xcomfiles
... etc.