Studying peer relationships is crucial in solving complex challenges underserved communities face and designing interventions. The effectiveness of such peer-based interventions relies on accurate network data regarding individual attributes and social influences. However, these datasets are often collected through self-reported surveys, introducing ambiguities in network construction. These ambiguities make it challenging to fully utilize the network data to understand the issues and to design the best interventions. We propose and solve two variations of link ambiguities in such network data -- (i) which among the two candidate links exists, and (ii) if a candidate link exists. We design a Graph Attention Network (GAT) that accounts for personal attributes and network relationships on real-world data with real and simulated ambiguities. We also demonstrate that by resolving these ambiguities, we improve network accuracy, and in turn, improve suicide risk prediction. We also uncover patterns using GNNExplainer to provide additional insights into vital features and relationships. This research demonstrates the potential of Graph Neural Networks (GNN) to advance real-world network data analysis facilitating more effective peer interventions across various fields.