Local traffic control schemes fall short of achieving coordination with other parts of the urban road network, whereas a centralized controller based on the detailed traffic models would suffer from excessive computational burden. State estimation for detailed traffic models with limited observations and unpredictability of individual driver behavior create additional complications in the applicability of these models for large-scale traffic control. This point toward the need for designing network-level controllers building on aggregated traffic models, which have recently attracted attention through the macroscopic fundamental diagram (MFD) of urban traffic. Under some conditions, the MFD provides a unimodal, low-scatter, and demand-insensitive relationship between vehicle accumulation and travel production inside an urban region. In this paper, we propose MFD-based economic model predictive control (MPC) schemes to improve mobility in heterogeneously congested large-scale urban road networks. For more realistic simulations of urban networks with route guidance actuation-based control, a new model with cyclic behavior prohibition is developed. This paper extends upon earlier works on perimeter control-based MPC schemes with MFD modeling by integrating route guidance type actuation, which distributes flows exiting a region over its neighboring regions. Performance of the proposed schemes is evaluated via simulations of congested scenarios with noise in demand estimation and measurement errors. Results show the possibility of substantial improvements in urban network performance, in terms of network delays and traveled distance, even for low levels of driver compliance to route guidance.