Is draining and washing an option? Not familiar with plaster. So sorry your having such a problem!!
Water table is way too high here to safely try that.
I agree that you should wait until you finish the SLAM before you worry about the stains.
I have an old plaster pool that is beyond the point of needing to be resurfaced and a pool cover that should have been replaced a long time ago, too. My plaster is stained by leaves when I open each year. The best way to get rid of this type of stain is very rigorous brushing with a stainless steel brush while the FC is at shock level. The stains are not like algae blooms in that they do not use up a lot of chlorine. I find that I work on the stains as time and my arms allow... it can be arm and back breaking work.
Unfortunately, I spent 10 minutes scrubbing the H#ll out of a one square foot section of stained plaster on Saturday (the section where the six pucks are now currently sitting) with my stainless brush while keeping the FC at 30% above what was called for in a Mustard Algae SLAM and it literally had zero effect on the stain. I came back out in the morning and it looked exactly the same.
So far the only thing that has affected the stain at all was to brush the plaster for about 20 seconds and then to leave a Tri-Chlor puck on the spot for 6 or more hours. That seems to burn out the stain.
The other alternative is to drain and acid wash which is expensive and will remove another layer of your aging, thinning plaster.
Again, water table in west Houston (especially with all of the rain we have had over the past month) would make attempting that extremely dangerous.
Also, I haven't actually stopped SLAMing the pool, right now I have gone ahead and raised the FC level to well over the recommendations for 50 CYA (FC is currently up at 38+) so if anything I have basically doubled down on the SLAM in the hopes that it would make a dent in both the stains as well as the continuing cloudiness.
I guess that SLAMing it and ignoring the stains is an option, however while I could potentially learn to live with the stains for the rest of the year (current plan is to remodel the pool next February) however I wouldn't want to have gone through 4-6 weeks of SLAMing the pool (basically half of the summer) just to potentially have algae come right back from the stuff left lurking deep in the stains.
Also,
if the continued cloudiness in the pool is being caused by particles slowly coming up out of the stains then won't the criteria for finishing the SLAM essentially never be met? Or am I just taking the "Clear water" condition too seriously?
I am asking because I really don't know.