Four lesser options, one major one.
Fast-forward the split party part. Don't dwell on stuff as much as you otherwise would.
Snack and bathroom break time. Shoo the other players off. This will serve as a cue to the sneakers that they should include everyone eventually.
Metagame, encourage the group to find ways to include people even when it's suboptimal.
Spring stuff on the other party to keep them occupied. Sure, if they just get a lead, they can wait to follow up, so make the action come to the PCs - someone kicks down the door or otherwise looks to interact with them NOW.
Give them all equal spotlight time. 5 minutes dealing with sneakers or interrogators, 5 with the others. They'll either start going to do stuff of their own accord, or they will, heaven forfend, roleplay with each other.
Number 5 is really my favorite. We've had plenty of great moments while half the party is doing something "important" and the other half goes to a bar and gets in trouble. All you have to do is give them the spotlight time, PCs are notoriously twitchy and impatient and will find ways to entertain themselves, "on task" or not.
My added thoughts based on your question edit.
You don't need to balance "in game" time. If one group went and did something for six hours, but real time that took five minutes, then you just need five minutes of spotlight time for the other group, even if that's five minutes of rousting a hobo and then 5:55 of "we go somewhere and hang out."
If they need ideas for what to do or you want to spring things on them - that's why God created random encounters, right? Either they self-motivate some mission oriented stuff, which you come up with, or they mess around in a tavern or go shopping, which you come up with, or they sit around looking glum till a land shark attacks them, which you come up with. You do anything you'd normally do to the full party, but ideally with slightly less kill. (Or not, if you want to dissuade them from splitting in the future.)
If they are content to wait in the bar, let them wait in the bar. Have fun bar things happen. People hang out in bars in real life, it's fun. And sometimes good and/or bad things happen, hence the larger than usual incidence of hookups and cop interventions in bars. All you need is for them to all be having fun and getting roughly equal "spotlight time" (time they get to actually do something at the game table).
Not everything has to be mission related or be a "subplot." They can just find out interesting things about the world they're in. If every story everyone ever tells them is a "subplot," then you get into a bad rut where their expectation is that anything that happens in the game world is FRAUGHT WITH MEANING, and it can't just be some guy BSing about how he fought a troll armed with a spoon once.
In my campaign, I make sure there's a healthy amount of "the world doesn't revolve around the PCs" stuff going on. Not only does it make for a realistic feel, but then when someone wants something to do, they have the expectation that "Hey, I can just go out there and go shopping, or find a bar, or find something to do - I don't have to be 'working through a plot element'" every damn minute of every damn day.
In my Pathfinder campaign recently, the party split. One half was going to do something on task and important. I don't even remember what it was and they probably don't either. The plan was to meet up at a known bar later that day. The other half of the party decided "we'll just go wait at the bar now." I roll a random encounter - giant cockroaches. They get to the bar, and the owner, "Ball-less Bill," an old ex-pirate with one leg, one hand, one eye, and apparently less then one thing down below, was standing outside the bar holding the door shut. "What's the problem?" "My basement flooded and there's these big ol' cockroaches running around in there! They're as big as dogs!" "We can take care of this! Stand aside, Bill!" The two PCs bust in and the cleric casts Call Lightning. The cockroaches are like CR 1/4, so they run all around and out into the street as the cleric blasts lightning holes in everything in sight. The fear of God is put into the local yokels, and the cleric gets an Infamy Point (the equivalent of a Hero Point in my pirate-oriented campaign). They yell "Wooo!" and go in and drink for free.
The other half of the party... They did something on mission. Got some information or something. Who cares. No one remembers that, but they remember the Great Roach Holocaust.
If you have proactive players, this shouldn't be a problem. If you have reactive players, then don't treat them like proactive players and give them 'things to follow up on.' Have the world turn, and its events happen around or to the players. If they decide to just go find another bar rather than chase out the giant cockroaches, fine, then make them choose whether they're drinking "bloodwine or dwarven grog" and go back to team A. Seems to me like you're overthinking this by requiring all events to be part of some big Mythic Plotweb.
I've run into this problem personally, and it can be quite difficult to cause limit breaks with any frequency. Challenging PCs to act against their virtues is definitely one way to build up limit, but there is one core source of limit you've skipped in your list:
Each virtue flaw has specific limit condition that, when met, forces the character to roll that virtue and gain limit equal to that amount
For example, if a character has the Deliberate Cruelty conviction flaw, they will be forced to roll conviction and gain successes when they are in particularly dire circumstances. Because this often results in several points of limit I find this to be the most effective way of causing a character to limit break.
Each PC is likely going to have a different flaw, so you'll need to make a list of them and watch out for those circumstances. Try to write stories that cause them to occur and don't be shy about making players roll. You'll have them breaking in no time.
Best Answer
Talk to your players about your constraints as a GM
Ultimately this is an issue where the party as a group of human individuals playing the game will need to make concessions in their play approach to the limitations of you as a human individual GMing the game. In a perfect world you'd be able to respond to their decisions instantly, allowing you to juggle GMing the two separate groups simultaneously, but from your description this just isn't a possibility. Sit down and talk with your players in person, outside of a game session and explain that the overall quality of the game will be improved by you being able to focus your efforts on the party as a singular group vs. a bunch of individuals or two groups. Naturally the party will split when the need must arise, but you can specifically prep/plan story points where this is indicated (the engine room is on fire AND there are enemies boarding our ship) as a way to signal to the players that this is a split which you are prepared to handle GMing.