Hello Marilyn -
1. 'All she was doing was nothing but crying all day' doesn't sound so strange to me.. '' all' seems to emphasize the message.
2. (a) We did nothing but running for gym in high school.
(b) We did nothing but run for gym in high school.
(c) She did nothing but crying the whole afternoon.
(d) She did nothing but cry the whole afternoon.
Earlier I had asked about the correctness of 2c because I feel that 2 a-d are all correct. I think I hear 2c construction type in popular music.