just a thought...I'm new to distilling and haven't had taken a break yet...but have a SS kit too and am thinking that SS kit would benefit from passivation treatment once in a while. For your situation would seem the last run of the stilling year would make sense. The passivation step is intended to dissolve any surface contaminants (iron surface contaminant that is leading to the rust spots) leave behind a protective chrome oxide surface layer. Time to air dry to form the protective layer is part of the process.
From the homebrewing forums you want 4% citric acid solution (40 grams per liter) at 100-140F with submersion time of 2 hour for 304 stainless. Lots of people point to a presentation that was published by NASA in 2013, linked here:
https://ntrs.nasa.gov/citations/20110001362
Complete cleaning protocol would be:
clean with hot PBW or similar
rinse with hot water
passivate with citric acid solution
rinse with hot water
air dry (important step, this is when the chrome surface layer is developed, minimum 24 hours seems to be recommended)
For start up some months later I believe all you should need to do rinse the dust off with water and get to stilling. Unless you see rust spots again. Hopefully you prevented them instead of having to clean them.
My understanding of the whole acetic acid wash followed by sacrificial run is designed to remove flux and machine oils that may be left behind following new equipment fabrication.
Challenge may be finding something large enough to contain your still during passivation. Hopefully it breaks down into small enough pieces to fit in a bucket/kettle for the passivation but might need to figure out some form of CIP using pumps and possibly spray ball. I do that for my SS fermentor.