Why did Ross change the sound-effects on the guns? Did he do it based on his conversation with Nojah and Sarahon about editing minecraft sound-effects? I mean I know he explained it and that Daniel was the one to do it, but why would he decide now would be the best time to change it after almost 50 episodes?
He's gone back to using the normal sound effects.
He didn't. His assistant that edits the sounds did it at his own initiative. Ross was suitably impressed and made a poll on his website asking if he should keep it for future episodes, use the normal sounds, or the third option was to show Ross cat picture. While the new sounds got majority vote, it was a very close poll, so he opted to use the original sound effects.
In one of the earlier Shephard's Mind episodes, Shephard is knocked unconscious and starts mumbling about Freeman, but at that point he didn't know that Freeman existed.
He could just know someone else with the same last name.
How is Gordon in such good shape physically? At best he's a borderline alcoholic who experiments with drugs and sometimes skips meals in favor of junk food. At worst, he's a full-blown alcoholic and druggie whose diet seems to mostly consist of hard liquor, vending machine snacks and whatever meals he steals from his coworkers. His (lack of) work ethic also makes it rather doubtful he keeps up an especially demanding physical regimen. Yet somehow he's able to navigate the gigantic maze/obstacle course that is Black Mesa, all while wearing a (presumably at least somewhat heavy) metallic hazmat suit.
His job involves spending a lot of time in that suit, his personality and comments about his past suggest a lot of zany antics and he vocally takes pride in how he's much more physically fit than the rest of the scientists. It's not that improbable that he either works out a lot or has spent so much time wearing the suit that he's able to do a lot of physical feats with or without it.
That, and we all know that one asshole who can down all the drugs and alcohol, function exactly the same, and wake up ready to go the next day. Gordon is that asshole.
I could buy Gordon not remembering Barney or the other Black Mesa staff, but why would he not recognize Dr. Breen, his own boss?