A couple of thoughts / observations / guesses. I can't diagnose from this sample of results, but maybe you have a slight bellows leak, or maybe you got some light stuck film from the GraLab timer's luminescent dial. Three feet seems kinda close to me. I'm pretty casual about how dark a darkroom should be, but I wouldn't get near that close.
I don't think the presoak is necessarily the culprit for the density variations on your film - but maybe it could be - I wouldn't use a presoak as a holding tank as I unload film. I'd unload all films completely, then presoak all for same time, agitating to prevent films from adhering to each other, then move to developer etc... Keep everything uniform. Who knows what the difference between a thirty second, or a three minute presoak is. Adding one more variable to the process is akin to asking for issues. Add to that, the chance that without initial agitation, films might start to stick together.
The inky colored presoak water is probably just sensitization dies or anti halation dye leaching out of the film.
Maybe your scan boosted the shadow contrast, since your shadows don't look as bad as you describe when I look at the reproduction online.
Best,
C