Ran the 3.0 out of fuel. Help

Recently ran the 3.0 out of fuel. A few warning lights came on, oil pressure, electronic accelerator, the yellow swirly, and check engine. System stayed primed, and got her to fire right back up once I added some fuel, but check engine, oil pressure, and [bolt] light still on at start up but go away. Check engine stays on. Can someone help me, I talked to one guy and he said it just needed to be cleared, and that nothing else should have caused any issues. Any help on the subject please....