If you are using Stage, definitely open the Project Browser to the code-block with all the stages (could be $Main or something else). Turn All Status ON. This should highlight the code blocks that are currently running in the PLC, along with what Stage are active (they will be highlighted in CYAN, like contacts).
This should help debug the "high level" control. So, go to RUN, then go to PROGRAM, then back to RUN and see what your code blocks and stages do.
If the code block with the stages is not CYAN, or if the specific stage that has Modbus instructions are not CYAN. The stages may flash quickly if they are working correctly and transitioning, but the stages may "hang" and remain CYAN if the Modbus instructions are timing out.
You get instruction level status in Ladder View, but the Project Browser status definitely helps you with the "high level" control debugging.