Excellent, you're going to love this!!
My advice (based on experience): If you can, take your guitar to a good luthier / guitar tech and get them to do a complete setup. If the nut is too high, setting it to the right height will make the guitar play much better. Additionally, leveling any uneven frets will also help. I think with cheaper guitars, most of the money is saved on the fit and finish so they pass that cost onto the consumer.
In the case of my Juggernaut project, I ended up having the neck angle adjusted in the pocket as well as the nut filed down. The guitar played WAY better after the work was done and yes, it started sounding like twice the guitar with the nice pickups.
You are changing your pots too, right? You "CAN" put caps in but I just wired volume knobs directly to the output on the guitar. Who needs a tone knob on a metal guitar anyway!?