I'd set the tone controls to flat on the receiver.
Phono IS different - it has much more gain and a heavy RIAA EQ curve to compensate for deficiencies in vinyl. Your signal will be distorted, bassy, and dull using that input.
I use the 1/4" out for my similar setup (and the impedance is a better match), but you could get away with the headphone out.
You can tweak with global EQ, but cabinet and mic settings should get you close. Yes, using a mic model will get you closer to what you're used to as recorded guitar tones.
Don't sweat any theoretical EQ adjustments for those specific speakers. They interact with your room in a way that is specific to your speakers, with your placement, in your room, in your listening position. So tweak it to your own ears, maybe using recordings you like as a guide.
