I'm thinking Natasha came to S.H.I.E.L.D. in the late nineties/2000ish. I use 616 canon as her actual history that comes to light during the Winter Soldier data dump; she's in the Red Room in the late 40's, super soldier serum'd, etc. I use the MCU canon as what's in the surface paperwork.
I was thinking with Clint that the majority would come from Comics, but to fit MCU.
He was abused at home by his dad, mom not there. Ran off with his brother when he was young and ended up at the circus. He and his brother ended up criminals. However to diverge into MCU, as a teen, Clint was offered a job by S.H.I.E.L.D. before he ended up a "hard core" criminal. At the same time SHILED ended up recruiting him, he entered a romantic relationship with Laura. As per MCU, He kept her hidden from everyone but Fury as their relationship progressed. With the flashback, Clint's dating Laura. With the current time, he's obviously married w/ kids. He has three kids: Cooper Barton - Son
Lila Barton - Daughter
Nathaniel Barton - Son
While dating Laura he did end up cheating with Bobbi Morse, and nearly destroying their relationship. However it was able to be mended. Bobbi ended up marrying Lance, but she has never quite forgiven Clint.
I'm avoiding dating Clint's timeline to allow for things like Pizza Dog, and appearances of Kate, Barney, and others.