Didn't Bert have an aunt in an episode? I cannot remember, but I remember Bert having an aunt. Maybe she is a character who is never seen.
Waldorf also has a sister named Astoria.
About Scooter and Gobo, I completely agree, maybe one of his parents is a fraggle. Red kind of also looks like Skeeter, so there you go. I also see a little resemblance between Boober and Gonzo, Mokey and Big Bird, and Wembley and Kermit, but none of those are obvious. The connections are more with the facial expressions than the physical aspects.
I also keep on going about Ernie and Lew Zealand being distant cousins, maybe they are brothers, but either could be logical, since they look nearly identical.
Gonzo and Grover kind of also look like they are brothers.
I might be missing some, but do not forget they were all created by Jim Henson, so every muppet bears at least some resemblance to another.
Muppetmonster