Theres a lot to alternate picking so its hard to know where to start but I will say this.
1) Learning any thing by Nuno Bettencourt is great. That man is a master rythm guitarist, lead guitarist, acoustic guitarist and songwriter/composer so you can learn God knows how much technique just learning his songs if you never learnt any one elses ever again!
2) Consider using a metronome and play at a speed where you are comfortable and then just keep knocking it up 5-10bpm when you can nail it. John Petrucci recommended some times knocking it up say 20bpm or more and coming back down which makes it easier. Some times you just have to go for it and not always practise slowly!
3) Always carry on when you make a mistake. If you stop youll never learn to get the flow right.
Sadly I think its just practise. Id recommend instructional videos by john petrucci as that seems to be aimed at intermediate players and above but if you get some thing by steve morse or al di meola even though its advanced youll be able to pick ideas out which will help you.
BTW it doesnt sound like youre that far off so keep at it.