Well, all bullshit aside, the 408 will be the better motor.
There's no magic in anything. Same air. 408 cubes is a hell of a lot more than 302 cubes. The 302 would have to be a lot better than the 408--and it won't be. No Cleveland head will be better than what you can get for a Windsor. A 4V Cleveland head would be worth a go--I kept a set up unti about 6-8 years ago when i finally decided I would never build that psuedo Boss 302 and sold them on Ebay.
400hp out of a 302? There's horsepower and then there's horsepower. At one time I calculated the Mean Effective Pressure MEP in a whole bunch of engines--carb, EFI, 4-valve EFI, turbocharged and diesels. It's a kind of theoretical yardstick to compare motors. You can goole MEP or BMEP if you want to know more. Anyway, I used the SAE NET ratings. I found that the best carbed motor made 108psi and the worst made 84psi. If you want to make 400hp with a 302 you need to buzz that baby to 9,500rpm, and the whole system needs to be tuned to run 9,700rpm so it is making it's best power there. You need 4V Cleveland heads with some serious work on them, you need a Holly Dominator 1050cfm carb and a suitable manifold. That 400hp is probably equal to 500hp on an engine dyno because the manufacturer publishes NET--it's as-installed.
Adding throttle body injection--like a Holley Procharger, the MEPS climp up to a 120psi range. That drops you all the way down to 8,700rpm. That's a lot better.
Adding a full-boat MPFI system like what you would find available for a 5.0--you can get 400hp at 7,500rpm with a 140psi MEP. That's going to involve throwing away the Ford parts.
Keep in mind, the 5.0 ran damn well making 225hp at around 140psi MEP--you want to close to doube that. You aren't going to double the MEP--you just want to maintain it and move it up the rpm scale until you get the the horsepower you want.
Now, with a 408cid engine you can have a LOT tamer engine that puts out the same numbers at lower rpms. To run a full-boat MPFI 408 at 400hp--you only have to spin it 5,500rpm. A 302 engine needs 7,500.
If you want to run a carb, you'll need 7,200 with a 408.
Yeah, you can show me dyno runs that are GROSS where such an engine made X number of horsepower. That doesn't compare to what current manufacturers publish. When a stock 4.6 Mustang with 300hp spanks your 400hp Heinz 57, you'll know why.
Always go for the cubes first. That's where your hard earned money gets the most return. Not patching some crap together.
After the cubes, then think about where you are going because you need the heads next.