[johnmarcus]

I think for your software product, you may have underestimated the value of GitHub.io domain. Your post makde it sound like it went from one custom self owned domain to another, that's not the case at all. I would move it back to github.io, and build your other domain over time until they are 1&2 in results (or there abouts)

[auganov]

Had exactly this experience. Had some very popular content up on a platform site, ranked very well. Wanted to move to my own domain. Found it nearly impossible to show up in search results at all. Even searching for the exact title wouldn't bring it up despite seemingly being "indexed".