Sorry in advance if I say anything that you don’t need. I am just kind of mentally running through everything.
On the low mic level: 1) Did you turn up the gain on the focusrite? An SM57 will take almost wide open gain on mine. 2) Is the pad button off? That is for hot signals (so you want it off for the mic). 3) Also check the instrument button. I don’t remember which way it should be, but you could try it both ways. 4) Move the mic closer to the instrument
On the hot line level inputs: 1) Turn the pad button on. 2) Instrument button off. 3) Adjust the gain
On mixing the levels… you don’t have to adjust the input signal to balance. You can adjust the levels during playback. So with recording each part, set the gains to get a decent signal without clipping. Then use the software to balance the levels on playback. If desired, you can “automate” the volume so that it changes levels for different parts during playback.
Looking forward to hearing it!