Whenever I read about the suits going from Toho to Tsuburaya the word "lent" or "borrowed" is always used. I have no idea if Tsuburaya had to pay a fee or what not, but it wouldn't be too surprising. Then again Tsuburaya was quite powerful and influential, so who knows.
All the modifications were made by Tsuburaya's team. I know they also borrowed the Baragon suit for Ultraman and modified it before returning it to Toho for Destroy All Monsters. It was in pretty poor condition though which is why Baragon wasn't really used in the film. The 1965 Godzilla suit was likely returned and cleaned up in some capacity since it was used for water scenes in Son of Godzilla, Destroy All Monsters and Godzilla vs. Hedorah.
"'Nostalgic' does not equal 'good,' and 'standards' does not equal 'elitism.'" "Being offended is inevitable. Living offended is your choice."