Not that I recall.
But I can name quite a few characters who never appeared together or had any scenes together.(At least not to my knowledge.)
Oscar & Harvey Kneeslapper
Big Bird & Harvey Kneeslapper
Ernie & Grover
Oscar & Prairie Dawn
Biff & Fat Blue
Fat Blue & the Count
The Count & Harvey Kneeslapper
Fat Blue & Oscar
Harvey Kneeslapper & Biff
Biff & Grover
The Count & Herry
I can also name some characters that would not have appeared together(at least not normally)due to being performed by the same muppeteer.
Big Bird & Oscar
Bert & Cookie Monster
Bert & Grover
Grover & Cookie Monster
Ernie & Kermit
The Count & Fat Blue
Fat Blue & Farley
Ernie & Guy Smiley
You made two different lists, with the second one listing characters who wouldn't have interracted due to having the same performer, but the first list features quite a few characters with the same performer (Biff and Fat Blue, Hery and The Count), but I know that some of the characters you listed have interracted on the show. Somebody has already mentioned the interractions between Ernie and Grover, so I'll list other interractions:
Big Bird & Harvey Kneeslapper - they (along with Herry Monster) sang "Ha, Ha, Ha" in The Muppet Alphabet Album (I don't think that song was ever made as an insert on the show, though).
Fat Blue & Oscar - They briefly interracted in Elmo's Sing-Along Guessing Game.
Biff & Grover - I've read about a sketch where the two appear as cavemen, inventing the wheel
Big Bird & Oscar - Out of all Muppets performed by the same performer, I think they interract the most. They have had major conversations in Christmas Eve on Sesame Street, What's the Name of That Song? and A Celebration of Me, Grover! and have briefly interracted in Follow That Bird and Elmo in Grouchland. Even after Matt Vogel has become an understudy for Big Bird, it seems like Caroll Spinney still performs both voices whenever Big Bird and Oscar interract.
Grover & Cookie Monster - There have been times when they interracted (back when Frank Oz was their only performer). They both sang "I Whistle a Happy Tune" together. I've read about a sketch with them at Muppet Wiki, and saw a picture from that early sketch, but I don't remember much about what hapened (I think it involved either a mystery box or a bell). There was a sketch where Cookie Monster told Ernie that he was on a diet, and wouldn't eat cookies, until Grover appeared and told Cookie Monster that he looked too sick (I think that Bert should have been used in this role; After all, the sketch took place in Ernie and Bert's apartment). And they also appeared togetehr in the song "Fuzzy and Blue" (though they didn't talk to each other).