The lag seems pretty random to me too and I think you might be right about the thrusters. My ping shouldn't read 67 if it is a red connection which tells me that something is probably bogging down the server. Maybe it's multiple people with multiple battleships that is causing it. It can't hurt to disable the NPC thrusters for a few days to see if it fixes the problem.
I have noticed though, that resetting the server usually gives a good 3-4 hours without any lag. Does multiple logging in and out bog down the server? I have noticed people logging in and out constantly to reset bribes at bases (I didn't know that that worked.) and then I get a red warning after a couple hours of playing with no server reset.
There is definitely something causing the lag problem because I find EVERYONE is lagging at the same time. The thrusters seem to be a good place to start.
Overall though the Discovery Mod is wonderful. The only "mod related" problems (besides lag) I have run into is Jump Holes and Bases not appearing on my Nav map but I can live with this.
