First off, Fuck am I jealous of you players. I'm the only one who ever runs Modern so I never get to play it. I do run it quite a bit though so I share what I do.
Random Encounters can work great but never have it be "You are attacked by 2d6 baddies". After a while it just doesn't make sense in a modern game. The enemy's are going to attack differently after a while. Going after the players money, destroying their vehicles, stuff like that. The idea that they would simply openly attack them all the time doesn't make sense. Even if it's a "random" fight it still fell's weird as a player. My advice would be to come up with a list. Treat random encounters like those little side characters you meet playing the new GTA games. Some chick is trying to find her purse, A man is getting very VERY angry talking on a payphone, A prostitute propositions a player for a good time, An old woman is having a really difficult time parallel parking, Stuff like that. Keep the definition of what an "encounter" is kind of loose. In old games of D&D even a door was considered an encounter. That's the mindset I would keep here.
Invincible monsters: I think the term Invincible should be used pretty loosely. As in make them really REALLY fucking strong, but make some weakness more obvious than others. For example I ran a modern game a year ago that had Vampires. These Vampiers were very strong. As in the only way to kill them was to do double their maximum hit points to them in one round of combat. Later on in the campaign they slowly discovered that infecting a vampire with the blood of another vampire takes away their bonuses. Before they figured that out the players literally had to run over the vampire with a car, throw a grenade at the vehicle exploding it, and then empty their entire clips into it. The first time they came upon one getting high off it's mates blood, they simply put a bullet through its head and were like "You have to be fucking kidding me. This whole time it was that simple!", and it was great. Even later on the discovered that they were afraid of cats for some reason and would run away. Stuff like that. So give the characters crazy strength (but not undefeated by sheer brute force) but throw in some weaknesses that are strange enough to get the players attention.
When I would run my games I would kind of break each session up into two phases. In the first phase we would start the game off and I would find out what the characters are doing, kind of pick up with their lives and develop the sub plots. My players were pretty good with coming up with their own story's, so I guess I got luck their. In the second phase we would move on to the "main plot" of the story. What I would do is ask the players a week ahead of time what "thread" (I ran a conspiracy game) the players wanted to pull at. I would be like "Last week you guy's said you are investigating the weird shit at the school so that's what your doing." I found that it really helped keep things smooth. I would also sometimes drop hints for each phase into the other phases. As for specific plot hooks I'm sure I could figure something out if you wanted.
The final thing I'm going to leave you with are some "house rules" (I stole them from something) that I found are pretty much essential for running modern games. They are Chase Rules and Heat Rules.
The Chase Rules are important because you would be surprised how often that comes up. Basically you start the players off with a number of "leads". If they pass the required skill checks then the lead goes up, if they fail the lead goes down. If the players get a certain number of leads ahead they get away. The opposition can increase the difficulty of the check by succeeding on their check, if they fail the difficulty goes down. It's a pretty simple mechanic, but it's absolutely necessary. It's the nature of chase scenes being kind of hard to pull off because you can't describe everything as you go. That mechanic allows you to abstract it but still be descriptive.
Heat rules are important because eventually the players are going to discover explosives or something and their needs to be consequences to setting off bombs in a city. Again, you'd be surprised how often stuff like that pops up. Start the game off at zero heat, completely anonymous, and then come up with a few "prerequisites" for going up and down on the levels accordingly. Level 1 would of course have consequences for the players, like the cops are aware their is increased activity in a certain area or something. Actually writing out the consequences for each level can be pretty useful too. I like to use 5 levels, with level 5 being the Army sending in the Tanks or some shit. Also, it's useful to have a different heat rating for the different factions of your game. Each of them would respond differently depending on how interested they are.
If you have any more thoughts or questions I would love to help. I'm pretty bored today and I don't have much else to pick my brain over.