A circulant-based spatially-coupled (SC) code is constructed by partitioning the circulants in the parity-check matrix of a block code into several components and piecing copies of these components in a diagonal structure. By connecting several SC codes, multi-dimensional SC (MD-SC) codes are constructed. In this paper, we present a systematic framework for constructing MD-SC codes with notably better cycle properties than their one-dimensional counterparts. In our framework, the multi-dimensional coupling is performed via an informed relocation of problematic circulants. This work is general in the terms of the number of constituent SC codes that are connected together, the number of neighboring SC codes that each constituent SC code is connected to, and the length of the cycles whose populations we aim to reduce. Finally, we present a decoding algorithm that utilizes the structures of the MD-SC code to achieve lower decoding latency. Compared to the conventional SC codes, our MD-SC codes have a notably lower population of small cycles, and a dramatic BER improvement. The results of this work can be particularly beneficial in data storage systems, e.g., 2D magnetic recording and 3D Flash systems, as high-performance MD-SC codes are robust against various channel impairments and non-uniformity.