By replacing standard non-linearities with polynomial activations, Polynomial Neural Networks (PNNs) are pivotal for applications such as privacy-preserving inference via Homomorphic Encryption (HE). However, training PNNs effectively presents a significant challenge: low-degree polynomials can limit model expressivity, while higher-degree polynomials, crucial for capturing complex functions, often suffer from numerical instability and gradient explosion. We introduce a robust and versatile training framework featuring two synergistic innovations: 1) a novel Boundary Loss that exponentially penalizes activation inputs outside a predefined stable range, and 2) Selective Gradient Clipping that effectively tames gradient magnitudes while preserving essential Batch Normalization statistics. We demonstrate our framework's broad efficacy by training PNNs within deep architectures composed of HE-compatible layers (e.g., linear layers, average pooling, batch normalization, as used in ResNet variants) across diverse image, audio, and human activity recognition datasets. These models consistently achieve high accuracy with low-degree polynomial activations (such as degree 2) and, critically, exhibit stable training and strong performance with polynomial degrees up to 22, where standard methods typically fail or suffer severe degradation. Furthermore, the performance of these PNNs achieves a remarkable parity, closely approaching that of their original ReLU-based counterparts. Extensive ablation studies validate the contributions of our techniques and guide hyperparameter selection. We confirm the HE-compatibility of the trained models, advancing the practical deployment of accurate, stable, and secure deep learning inference.