#1
What type of pick up's would be a good upgrade if you like playing things by like three days grace and breaking benjamin for a Yamaha pac 012... H/S/S heard different pick up's are good for different types of music..
My Gear

Ibanez GSR 200
Schecter C4
Fender Rumble 100
#2
Seymour Duncan's are nice imo. Since your setup is H/S/S, you'll probably want SHR-1 hot rails for the neck position, and even the middle position if you wanted to go H/H/H. The SSL-4 is a pretty heavy single coil as well, which I have in the neck and mid position of a H/S/S guitar. For the bridge humbucker, anything with high output will work good. The SH-6 Duncan Distortion or SH-13 Dimebucker would be good. If cost is an issue, look into Mighty Mite Motherbuckers as well.
#3
Stay away from the Dimebucker. Muddy, terrible pickup. I've heard hotrails are muddy, but I haven't tried them.

The Seymour Duncan SH-11 Custom Custom will be a great bridge humbucker. Defnitely gives you the crunch for alt-rock bands like those you mentioned.

For the S/S spaces in your guitar...
Maybe a SSL52-1 Five-two in the neck, and a SSL52-1b Five-Two in the middle.
These have a better bass response than the normal single coils, so that might be good for what you want.
Why the bridge Five-two model (As evidenced by the 'b' in the model name.) in the middle position? More balanced output.