Well, as per the norm, I'm thinking about things more and may be coming back full circle.
I called up the machine shop on the heads. The heads are done but not assembled yet. I told them to hold off on assembly since I would be buying a cam kit with proper springs, so might as well let them assemble that. But those are good to go and the chambers are 56.5 ccs. Perfect for making about 10:1 compression with the short block setups I was looking at.
Then I called the machine shop I took the block to. They haven't touched it. I figured that was the case, said it would be a couple weeks yet. I know where this is going - they're not going to get it done in any reasonable amount of time. Time to call ATK on a short block.
Called ATK, they said they stopped selling the 331 short block entirely, and they actually don't sell 331s at all anymore, or any 302-based short blocks. They said they just have a hard time finding good 302 blocks and so the ones they do get they save for full on crate engines since there's more money in those. Totally understand and respect that. However their crate 351W they sell (which is $1k cheaper, and free shipping) is in stock, ready to ship. This was originally why I had thought I would go with a 351. More displacement, less money, and a stronger block/rotating assembly to handle the power I throw at it.
So then I went looking around at 331 stroker short blocks, and was reminded of one of the reasons I was going to go with ATK - they were the best value by several hundred bucks on what was already going to be a more expensive proposition. So that was a downer.
Then I called up Speedmaster to talk to them about their 8-stack EFI - basically EFI that looks like Webers. Originally, I had thought about going with a 351W also because their 8-stack injection is a really good value at around $850 including shipping. That still requires fuel injectors and a computer, but even factoring those in it's an easy $1k+ savings over Webers. I asked them about the fuel spitting issues that Webers have, and they said they've never heard of issues with that using their setup. While it wouldn't have the same sensitivity to needing vacuum like Webers do since the fuel is injected, I would imagine there would still be some sensitivity.
I'm back to thinking that a 351 is going to be the way to go for a few reasons. First, like I had originally figured it will save me money. I also now have a transmission that can handle whatever I can throw at it, and a 351 is going to be a lot tougher than a 302 which gives me some more freedom relative to power. Additionally while I do really want to do Webers at some point, my wife will be driving the car and I think she would appreciate the ease of starting that comes with EFI. I will have an extra 50 lbs up front but I'm cutting weight in enough other places that on the whole, the car will be lighter than a lot of 302 powered cars. The ability to also have some more flexibility for an off-the-shelf cam is also appealing rather than sticking to a super wide lobe separation angle. I really do want a good lope in there at idle. And when I ordered the kit, I also had planned on a 351 so I have 351 headers already. I was figuring out what exactly I was going to do with those. All around, this is a decision that will cost less, be easier, probably more durable/torquey, etc. The negatives are the extra weight - both in the block and rotating assembly - and also in having a bit less room under the hood to work on it. However, everyone who I talked to said they didn't find working on the 351 to be a problem at all in a Cobra.
It's Friday afternoon and I don't need any of this stuff tomorrow (nor would I get it anyway), so I'm not ordering anything. However I think I'm back to being settled on the 351. I'm going to think about it over the weekend some more and plan to start ordering parts on Monday. Input over the weekend while I'm thinking about all of this is welcome.