I have not had much trouble. I'm 80 years in so far, and it goes... REASONABLY fast. There is 1 or 2 NPRs, and most everything else does its own thing. I def. suggest setting to zero and let them appear as you meet them. Explore in one direction at a time. When you meet an alien, STOP. If you go a warmongering route-- well, they won't slow it down much. Cuz they be D-E-D-dead. Turn off invaders, at first. You can turn them on later for a fun event in your written history.
As near as I can tell, what has slowed me down the most is my civilian industry. They have hundreds of ships. I've addressed this in part by stopping them from building most vessels, except for quite large, quite expensive vessels. They buy them infrequently as each one is a major investment, but each can move larger amounts of cargo.
I would reccomend that every time you upgrade your freighters, add another 10 cargo spaces. Mine go in jumps from 5, 15, and now 25. (but those big ones are, as I said, really expensive at 100kt each with big ol' honkin engines, CIWS anti missile tech, and armor).
ALSO: SAVE A LOT.
The database is quirky. Full o' quirks. if you back up at least 3 times per session, and before exploring a new system, you can avoid lots of buggyness. I suggest a few nasty ugly games at first while you figure out really how to play-- being terrible at the game and playing it wrong i managed to fry the database a couple times. I keep six backed up copies of the database on file at all times, overwriting in sequence. This is done by CTRL+C CTRL+V ing the database and placeing them in different directories (mine are labeled 1-5)
ALSO: whats your field in g school. I finish G school in 10 days, chemistry.