Why Gaudiya Sampradaye followed the Kali Upanishad of Krsna Yajurveda.?
Nitaibol! Gaudiya Vaishnav here. There is no mis-interpretation of the Mantra at all. All the Gaudiya Acharyas, from the time of Lord Chaitanya have quoted the Mahamantra to be:
"Hare Krsna Hare Krsna, Krsna Krsna Hare Hare, Hare Rama Hare Rama, Rama Rama Hare Hare"
The change to Hare Rama first, was made in recent manuscripts by Ramanandis who wished to give more importance to Lord Rama. Actually, you will see, there are some scholars, like Jagad Guru Ramabhadracharya who despite being a Ramanandi, sings the mantra with "Hare Krsna" first. The oldest surviving manuscript we have of Kali Santarana Upanisad is a 17th century copy with the commentary by the Advaitin scholar Brahmayogin Ramacandrendra Sarasvati. It is only from this copy, that the "Hare Rama" appears first. However I doubt the authenticity of that manuscript because we see already in the 15th Century, people were chanting the Mahamantra in its correct order of "Hare Krsna" first. We know this because Dhyanachandra Goswami, in his Gaura Govindarcana Smarana Paddhati quotes Sanat-Kumar Samhita as follows:
hare-krsnau dvir avrttau krsna tadrk tatha hare hare rama tatha rama tatha tadrg ghare manuh hare krsna hare krsna krsna krsna hare hare hare rama hare rama rama rama hare hare
The words ‘Hare Krsna’ are to be repeated twice, then ‘Krsna’ and ‘Hare’ are to be repeated separately twice. Similarly, ‘Hare Rama’, ‘Rama’ and ‘Hare’ are also repeated twice. The mantra will thus be – Hare Krsna Hare Krsna Krsna Krsna Hare Hare, Hare Rama Hare Rama Rama Rama Hare Hare.
This is also the order of the Mahamantra found in scriptures such as Brahmananda Purana, Vayu Purana and also later Chaitanya Upanisad and Ananta Samhita.
It is natural that many people in other sampradayas will consider these references as interpolations . We can also say the same in case of them . We have the references intact from our acharyas who were true vairagis and need no interpolation to prove themselves . The whole world is a witness to their scholarship.
There are instances where Srila Jiva Goswami in his sandarbhas has referred to the scriptural quotes presented by Sri Madhavacharya without actually verifying them . Srila Madhavacharya is our sampradaya acharya . Sri Jiva had faith in the scholarship of Madhavacharya . Similarly our faith in the words of our sampradaya acharyas is intact.
Nowadays many references are lost in time and the world knows very well that only a few percent of the entire vedic texts exists today . So there is no point arguing with sastric references the acharyas provided 500 years ago . Some might be lost in time but the knowledge is preserved in their books and available to us. This is the importance of knowledge transferred through guru parampara . This is the importance of being connected through a bonafide sampradaya.