Thanks Matt for the reply,
As We didn't receive any manual penalty in GWT whether it is Panda or Penguin, that caused us drop our ranking of .com site. But after that we studied thoroughly by ourselves a lot in order to know first whole about SEO, all Google updates, guidelines , and best practices etc. And revamped our old .com website from scratch; whether it is about new site structure, best UX from users point of view, unique content, internal linking, meta tags, curating high in-depth researched article or blog posts, building quality & high relevant links etc
We also found many many suspicious backlinks as well here and thought to cleanup that as well may be the reason behind.
Yes, with keeping above all best SEO practices in mind to formed another new website https://example.org/ . BUT still we are facing STRANGE behavior to our website by Google, & not considered us to beat our competitors. We worked enough hard & done backlink profile analysis of our competitors and found many bad activities by them, still ranking in good position in SERPs than us.