I've been working on a themed USFIV video, where I showcase all supers/Ultras you can combo after in the latest version without trades, starting from 0 stun. I'm feeling quite confident that I have them all, but I wanted to post it here and see if anyone could succeed where I failed (For install/Passive moves one has to start it mid-combo and then hit with something after it's completely over. But I've already figured them out for everyone, even Makoto). Some explanations below:
FB: Can make a fireball connect during or after the Ultra (Lamest solution but I guess it counts so it's there)
AA: Can only combo from very specific Anti-Air situations (Also kinda lame but not as much)
Y: Yes
N: No
Stun: There's a valid 0-stun combo which allows you to combo after this.
>0 stun: Noticably you can combo after these when starting from more than 0 stun, but from what I can tell here are no viable 0-stun options.

Notes:
Adon U1 would've worked as an AA in Super, but not anymore with its slam knockdown.
Vega Super (Base): So basically his super combos into its own follow-up, which teeeechnically counts since they scale separately
Sagat: The Rose-specific post U1 combo and similar set-ups seem to have been patched out, removing any practical Post U1 combos
Seth:The suction effects of Super and U2 can combo into a sonic boom, super lame but counts
Dudley U2: Only works when you Rose FADC and then chip kill with the 2nd hit of U2, having the Rose connect after.
These are all I've managed to find solutions for. A few close calls where I felt really closebut couldn't make it:
Cammy Super (She reacts slightly different than U1 on AA which seems to make all the difference, really close but can't find anything)
Yang U2 (If you can get the final hit as an AA high enough you might be able to juggle with his 3f c.LK, but I can't find a set-up that gets the dummy high enough with Yang's lack of positioning control)
Vega Super (The claw portion)(I can get them pretty high with a 1-hit super, but not high enough for the 2nd hit of Scarlet Terror to hit. EX does, but that's obviously an illegal 5-bar combo)