Modify RU's
Locate the file "persist*.lua" where the * is the mission number. The file is in the "Homeworld2\Bin\Profiles\Profile\Campaign\ASCENSION" folder. Open the "persist*.lua" file with a text editor such as Notepad. Locate "RUs =" at the bottom of the file and change the value to whatever you like.
Modify Ships
Locate the file "persist*.lua" where the * is the mission number. The file is in the "Homeworld2\Bin\Profiles\Profile\Campaign\ASCENSION" folder. Open the "persist*.lua" file with a text editor such as Notepad. Locate any string containing the string for your ships (Example: Hwr_Bomber). Edit this one with ex. Hwr_AssulteCorvette, and your former bomber is now a GunShip. You can do this with all your ships, the only thing you have to find out is what the diffrent ships are named.