If the devkit is a DTL-H, the instructions are pretty much the same as retail systems. For DTL-T (e.g. DTL-T10000 or DTL-T15000), there is lots of info here, including a link to a disassembly guide: https://archive.org/details/ps2_tool_guide/
PhyreEngine doesn't use .NET, and it is written in C++ (with optional Lua for scripting). You might be thinking of PlayStation Mobile, which does use .NET for scripting.