Run, do not walk, and head for Nitro first! lol you don't have to run, although I did in a moment with lacking patience. Ride Nitro first, then you might wanna ride Batman: The ride because the line is long all day. Follow that up with Batman and Robin: The Chiller. After this I would usually run to Medusa, but Scream Machine is on the way. After Medusa do Viper (if it's open), Rolling Thunder, then Scream Machine if you didn't already ride it.
That would only be if you've never been there before and want to try every coaster. Since you're going for two days, it shouldn't be that hard at all.
My suggestions for the coasters and what I feel about them:
Nitro: AWESOME. Ride first. Amazing. That pretty much covers it.
BTR: Fun ride. Good B&M invert. Nothing really special about this ride, but it is fun. I wouldn't skip it.
Chiller: If both sides are open, ride Batman. I don't know if the lapbar rumors are true, but I'm pretty sure that the Batman side is running with OTS restraints. It's not too bad on the Batman side, the Robin side really throws you around sometimes. I always ride it anyway. If anything, you should ride for the launch alone. What a rush!
Medusa: First B&M floorless. I love this ride! If you can, wait the extra time for the front row. It really makes a difference. More intense, and more fun.
Viper: I'm not really a fan. TOGO coaster. It's pretty short. Has a good first drop. Painful afterwards. Ride if you must.
Rolling Thunder: Right side is rougher than the left I've heard. Because I've only been on the right side (just my luck) I can say that it is a bit rough, but hey woodies are meant to throw you a lil! Ride it for the fact that it's the only woodie in the park (They really need another). If it's racing def. go on!
GASM: Not that bad of a ride. A lil rough if you keep your head against the headrest, so ignore those warnings and move your head an inch or two away. The ride will be much more fun. Whenever I go to the park this one is a walk on.
Remember, there are plenty of great flat rides at Great Adventure too, as well as a couple of good extra pay rides. Have fun!