While I am unsure as to why you get the build error you are getting, I don't think you will find anything of value in the intermediary files between the assembler and linker. The .s file is a great intermediary file because it gives you the compiler-generated assembly code. From that point, it is just assembled into binary op-codes. You would not be able to glean any sort of pipeline bubble information or anything similar in terms of overall performance. Like Andreas said, if the pipe doesn't incur stalls, it is an instruction per cycle, and the multi-cycle instructions are covered in the app note that you are already familiar with.
-Joe