In my modern / near future hack I have been playing around with using a mission format based on the F3EAD Special Operations intelligence & targeting process. Feel free to comment.
Find-Fix-Finish-Exploit-Analyze-Disseminate
https://docs.google.com/presentation/d/1xpZ-VqJk1TcPOpquNAK4kMjwKV7YeNmp6gn9kgQ0rTo/edit?usp=sharing
I like the idea of adding potential consequence outside the “finish” or main point of action.
I am wondering about the targeting and heat racing clocks being 8 segments though. It might just be my own experience running BitD/FitD, but I would expect this part of the mission to take a long time and potentially use up a lot of the character’s stress before they even get to the finish.
It might be worth trying to ramp up the tension with asymmetrical or shorter clocks (6 targeting / 4 heat for example).
It might also be more fun for players to push against the goal as hard as they want. Instead of having a hard failure state after filling heat, you could have a series of linked heat clocks. The more of those they fill up the more trouble they get in or worse their position is when they get to the finish part of the operation.
Rough example:
Noticed (4 seg) (Risky position) 
Tracked (4 seg) (Desparate position) Interference (4 seg) (Reduced effect)
Or you could have a series of linked targeting clocks. The players can push for more information, at the cost of continuing to engage with the target and risk harm or trauma.
Rough example:
Gain Level 1 Intel (4 segment) Gain Level 2 Intel (6 segment) Gain Level 3 Intel (8 Segment) etc.
Anyway, all of this is to say it’s important to keep the action moving forward and let the players pivot mid-mission. If it becomes clear the players are likely going to fill the heat clock and not accomplish their goal, they might stop taking risks.
I like what you’ve got! Thanks for letting me brain-dump. 
Something I’ve been working on is instead of having wanted levels, use Heat as a GM currency that they can spend on the Magnitude table (page 220 of the book) to send new threats at the player characters whenever. There isn’t necessarily post-mission fallout, there’s just a looming threat of the GM cashing in a boat load of Heat on a huge threat, labeling it with details from previous missions (the guild you pissed off a mission or two back has gotten wind of your activities and sends a punitive strike force to get even), and then force the players to neutralize the threat or carrying on with their daily operations while the threat looms.
For example, the player’s crew has 14 Heat they’ve built up and the GM decides to finally cash in. For several days (5 heat) the PCs and their holdings will be attacked by small gangs (1 Heat) of goons with excellent gear (3 Heat) and will be chased across an entire district (5 Heat) if they are detected by one of these gangs. Naturally, only one gang a day will be a problem, but they’ll continue to be a threat or nuisance for the duration of the threat.
This is how Dusk City Outlaws uses heat. It works well. The biggest issue is that it takes away the long term consequence of generating heat.
This is an interesting point. In my system you’re meant to hope about from star system to star system and your group does (at least ostensibly) have some kind of sanction to perform particular extra-legal activities, so the heat they incur would be faction-facing instead of police-facing. Chartists have their Charters of Trade, Mercenaries have their Chronicle and Bonding, Academics have Grants of Research, and even Shadows, Assassins, and Vigilantes will have some kind of documentation that ostensibly allows them to exist on paper regardless of what their true activities are.
Regardless of that point, I should look again at the mission fallout mechanic and see if it still makes more sense than the proposed heat expenditure method.
After a bit more thought, you could just use faction status to track long term consequences.