Just as an update to this, I did manage to sort out my problem! I went to the Argyll CMS mailing list, and I got some help there. Here's a link for anyone interested: https://www.freelists.org/post/argyllcms/Very-poor-results-with-1000-patch-target,18
It turns out that my initial scan with my 1000+ patch target had many bad readings, most likely due to the small size of the patches. My results were as follows for colprof:
peak err = 37.499292, avg err = 0.889221, RMS = 2.756460
After making a new ~520 patch sheet with larger patches and scanning them in, I got these results upon running colprof:
Peak err = 1.633284, avg err = 0.377664, RMS = 0.441556
Much better. I'm now able to print as accurately as ever. ALSO, I can confirm that the ColorSync app DOES produce a reliable color target. There was absolutely no noticeable difference between the sheet printed with Adobe Color Print Utility and ColorSync.