I'd recommend buying the red comet cars. Buyer's remorse is likely to happen if you don't go all the way in on this, especially since you may not be able to find the cars easily later on, at least while this is relatively new.
Buyer's remorse is common when we buy these things. We always find reason to second guess ourselves. One of the first people I met in this hobby was a fellow at least 25 years older than me. He told me that money can be replaced, but sometimes you have to take the opportunity to buy something when it arises. Now that doesn't mean spending beyond your budget, but you're talking the difference in price between one set of cars and another. Something to think about.
The whole notion of the 400E being too large for the cars is kind of silly. There is absolutely nothing scale about anything tinplate, prewar or reproduction. It's really just a personal preference, and while a 390E may look more "prototypical" than a 400E, as far as proportion, the 400E will always draw more attention. The same goes with the comet cars versus the 418 cars. Yeah, the 418's are a little taller, but all the features on the comet cars set them apart.
I'm no statistician, but I'd make a guess that the 400E Blue Comet is one of the top two or three most easily identifiable trains that come to mind when people think Lionel standard gauge, not the 390E version. So, it's all about how you feel concerning its looks and cost, not what anyone on this forum says.
I'm not trying to sway you, but don't worry about what comments other people have concerning 400E's versus the cars. They've been mated together since 1931, and people still are attracted to them. And remember, we all post and read this forum, but in the end, when asking the opinion of contributors concerning what to buy, you're kind of asking strangers, to an extent, how to spend your money. Your opinion is just as valid and no less correct than any one of the contributors. And yes, I gave you my opinion. It's neither correct or incorrect. I just know that sometimes it's better to step up while you have the chance. Two months down the road, whether you spend $600 or $1000, you won't really remember the money.