You will need to get the nut slots opened up a bit to accomodate the heavier strings.

Once all of the physical adjustments have been done to set up for the strings, you might try installing a higher value of pot for the tone and volume controls. As a generalization, low values of pot resistance bleed off the treble, and high values allow more treble to come out.

Some factory Tone pots are made such that turning them up fully will actually disconnect the capacitor and the internal resistor, which is ideal, but aftermarket pots don't have this feature. So even at the highest setting, there is still some treble bleed-off.

The Volume pot is always across the pup output, so the value of this pot will definitely have an effect on the tone. Too low a resistance will make a pup sound muddy. Too high can sound screechy.

Even top-quality pots are less than $10 each, so it's a cheap way to tweak your tone.