Good project.
Note that you don't need to / shouldn't bother to simulate the crystal ; clock frequency is taken from the mcu property anyway so all you have is a performance hit.
The messages I get are warnings to do with GMIN stepping - means that the simulator is trying to compensate to achieve convergence. GMIN is a leakage resistance for reverse biased semiconductor junctions and other theoretical points of infinite impedance. Lower values make the circuit look more and more like a network of resistors (which will always solve). But this is at the expense of accuracy. The default is 1E-12; values above 1E-9 will give fairly meaningless results.
If you want, you can turn these messages off from Debug Menu - Configure Diagnostics Dialogue - System Diagnostics.