Vinyl pool stains

Just opened my 18 x 36 in ground pool. Noticed some light brown stains primarily on the bottom. They won't come off with brushing. Added algaecide when I opened pool and have had ongoing problems maintaining pH. Chlorine level when I opened it showed 3 ppm. I figured it was probably metal stains so I dropped chlorine to near 0 and added 5 # of citric acid and circulated pool for about 6 hrs. The steps cleaned up great and some of the minor staining cleared up but major "blotches" of staining remain. Anyone have any ideas what to do next?