Well, this is the part where I get out of my depth, but my understanding was that there were some pretty big differences.
In d20 Modern, guns are pretty vanilla -- almost all handguns do 2d6, while longarms do 2d8 or, for the big stuff, 2d10. The differences are pretty minor -- one gun is mastercraft (+1 to hit), while another has a slightly longer range (40 feet instead of 30), and still another has a larger clip. There's really no "best gun", and people getting shot with guns isn't a death sentence (2d6 damage is only likely to threaten a massive damage check if you roll a critical). In CoC, I believe that guns are a fair amount more lethal, and since you're only trying to crack 10 on the massive damage check, that's even more deadly.
It's... well, I guess the right way to say it is "In d20 Modern, if you don't have several feats invested in something, it's assumed that you're not very good at it." So in theory, a goon with personal firearm proficiency can have a gun trained on a heroic PC, and the heroic PC isn't in that much danger -- the goon still has to hit him with the attack, and it'll only do 2d6 damage, which probably won't threaten an MDT on an athletic hero.
On the other hand, a major villain with some levels will be holding that gun on the PCs, and he'll have Point Blank Shot and Double Tap, and maybe Mastercraft +1 damaging bullets, so he'll be doing 3d6+2 (Double Tap adds 1 die of damage, PBS adds 1, Mastercraft adds 1), which is far more likely to kill a hero with a single shot.
Personally, I like this. I like my heroes to be able to take out a single lackey with a gun, while still comfortably nervous when confronted by ten lackeys with shotguns (2d8, and you know that one of them will hit). For d20 Modern, this is about the level of Heroic vs. Realistic that I want.
For CoC, though, you might want to have even high-level people be terrified of a single cultist with a gatling gun -- which, if I recall correctly, is one step from "okay, forget the damage, just save or die", for all intents and purposes. It's easier to threaten people that way.
CoC also uses different Autofire rules. I don't remember them offhand, but they are, well, different. I personally am fine with d20 Modern's autofire rules, but you might wanna see which one gives the right "feel" for your game.
EDIT: PS: Glad I could help. Sorry I don't know more about the details of the CoC stuff offhand. My players and I looked at it, played around with it a bit, and then opted to just go with d20 Modern plus Sanity, like you were suggesting. But that's because my players already know d20M really well. The situation could be hugely different for people new to either system.