Gurudev, in the Vedic period, there is no mention of the presence of Lord Brahma, Lord Vishnu and Lord Shiva. The period between 3500 BC and 2800 BC is said to be the Vedic period in Indian history; that between 2800 BC and 2600 BC is called the Age of Ramayana. In this entire stretch, there is no mention or evidence of the worship of Lord Shiva. So when exactly did the tradition of worshiping Lord Shiva begin in the form of the Linga and the Yoni, and why?
There is a book called Bharat Gyan which you should read. The period of 2,800 years that you are speaking about is not accurate. Lord Krishna was there about 5,200 years back and Lord Rama was there about 7,500 years back, and at least 10,000 years before that the Vedas had been conceived and written.
I suggest you contact the department of Bharat Gyan, or meet Dr. D.K. Hari. They will tell you everything about this. They have done extensive research in this area so they will be able to answer your queries.