Stuff on SD should be safe from a factory reset - that's where the backup apps back up to. But to be sure, by all means remove the card.
Slow GPS fix is a funny one. Have you tried an app like "GPS Status", which downloads GPS assistance data? That could speed the lock significantly.
I actually had my GPS performance degrade a lot once. Became very slow, and once it had locked the accuracy was worse than I remembered. I was changing ROMs a lot then so assumed it was related, but it didn't seem to improve significantly when I changed again. Turned out it was my case - I was using a leather flip case that had a bit of metal in the rim, just enough to interfere with the (very weak) GPS signal!