2000 Dodge Neon brake fluid?

Okay I had a huge mess with my 2000 dodge neon. I was driving on the hwy about 80 mph, I had just gotten $20.00 in gas (i was real low, it made me nervous) driving along when all of a sudden my car lost all power! The check engine light came on and just flashed once that I cought and wouldn't start back up. I had the car towed back home about 3 hours away and began troubleshooting and repairing.
all things that i've done are new spark plugs and wires-new pcv valve-new air filter-all new fuses-new battery-and new timing belt. I also went to dodge site and there are 2 recalls pcv hosing and brake booster cable. NOW I finally got my care to barely start but it dies right out. It's very hard starting and souds like an older engine that you have to pump on the gas peddle to get engine to fire. What else could be wrong with my poor car? The sensor was reset and actually no battery while it sat longer that 2 weeks, could it be that? I know sensor needs to relearn everything, HELP!