While typing this I see a reply from kratmel, who always offers excellent advice. I'll leave mine up to provide some additional general information.
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No time at the moment to go through your project(s) in detail, so I'll just share my approach. When I have multiple situations that require activating a coil, I will identify all those situations and place them in a single ladder rung so that I can use a single coil without sets & resets. Sometimes each of those situations are too unwieldy for a single ladder rung, so then I create intermediate coils that will substitute for each unwieldy situation. Then each of those intermediate coils can be placed in parallel to activate the final coil needed.
Set & resets I use for latches and sometimes to provide the opportunity for an HMI button to turn something on and off manually that will also be controlled by the PLC.
You are correct that you can lose yourself with too many sets & resets, so for that reason I avoid them except for the items mentioned above.