The installation procedure is easy. Just open the SPK file you've just downloaded with Cycrow's XScript Installer. If you don't use XScript Installer, you'll need WinRAR, 7zip or a similar tool to extract all files from the archive to your X3 Reunion installation folder. This done, please follow the following steps:
There's also a few other shortcuts (still at the bottom) that you may want to assign, you'll need them when you'll have bought some ship upgrades to the Guild. All Pirate Guild shortcuts are written like PG: something. Anyway, the plugin will remind you once you've bought the specific upgrade.
Upgrade process from a version to another may vary. Usually all you will need to do is to copy the files from the archive to the X3 Reunion folder and load your savegame as usual. The plugin will automatically update itself and send you a message when done. But if you notice any glitch, try to do the following :
Anyway read the post on the board announcing the new version, if you have anything special to do I will tell it there.
Pirate Guild has improved a lot since the 0.x versions, so you'll need to clean the old version before installing the new one to be sure you won't have any problem.
Before installing anything, run your game as usual, then :
You will need at least X3 2.0 for Pirate Guild to work properly. Pirate Guild should be compatible (meaning it won't overwrite ship commands or texts from other scripts) with most plugins and scripts. However my plugin make available about 10 new upgrades for your ships (and for the ships handled by the Guild). Some are similar to scripts written by other people. As long as you don't use two similar ship upgrades on the same ship in the same time things should go smoothly.
But if you like Pirate Guild, and want to have a good playing experience, I'd suggest you to use the ship upgrades from PG itself, even if the 3rd party may (or may not) be better. They have been written to work well with every aspect of PG, and moreover this time, your won't be the only ship in the universe to use those, as pirate Pirate Guild vessels will also have them onboard.
This said, there is one script called Friendly Pirates which is totally incompatible with Pirate Guild. The goal of this piece of code was to turn the pirates blue, so I take a wild guess than many of you tried this script at least once. You must remove it correctly before installing Pirate Guild. Check the Friendly Pirates topic on EgoBoard, there's a post here explaining how to remove it.
About Mods, there should have any problem, as long as the mod you're using has a few pirate sectors and PB. As a general note, the more pirate sectors and stations, the better. Pirate Guild will probably work better (but will also be a much tougher opponment) with the Terradine Mod than with most other mods, due to the map design.