I noticed a lack of posts in this forum. But for anyone interested, if you have the Ur-Quan Masters version, if you haven't found these already, there is a nice collection of fan made mods.
http://www.star-control.com/fan/mods.php
There are some that rebalance the game, remove/extend the time limit, and one that makes it way more challenging. I don't know if you can use them all at once or not, but I have several different copies set up with the different mods. Totally new experience for a few different playthroughs once you beat the original
