-Aluminum heads or iron?
Aluminum; big block guys get enough crap about weight...everyone wants aluminum heads.
-429, 460, 514, 521?
All of the above, and add combos for the 4.3 and 4.5" steel stroke cranks. I think you'll find that penis envy abounds and most folks will want "at least" a 514 since the motorsport crate has gotten so much press. That said, you could probably sell a "427" based 385 and make a lot of pseudo-purists happy. Even though it's the wrong engine (not an FE), having the correct CI is enough for some people. I know it doesn't make sense, but you wouldn't believe how many 385's I've seen with 427 badges on the valve covers. I'd do a small/medium/large approach. 427/9, 514, and 545. Offer forged steel cranks and forged pistons / good rods / 4-bolt mains / block fill, as an option for serious race oriented folks.
-Does idle quality/vacuum play a role for you guys?
Yes and no. Most cobras use vacuum brake boosters; so yes. The early ones were manual, so no. The newest developments are hydraboost...so no.
-Flat tappet or roller cam?
Considering the problems people have had with flat tappet wear and break-in, I'd offer roller as an option.
-Hydrualic or solid tappets?
From what I can tell, it's a rarity to find someone that cares about 6000+ rpm in a big block cobra. Solid would be an option for race oriented folks.
-Price point?
Most cobra guys prefer "right" over "cheap". If you're spending $40,000+ for a roller (sans engine and trans), you don't care much about saving $1000 on the engine.
-Manifold hieght?
Anything taller than a blue thunder dual-quad won't fit most cars unless you go EFI and do something like I did...which is unpopular. My car is considered an abortion to purists. Which brings me to a suggestion. Offer EFI as an option, turn-key.
-Aluminum water pump or iron?
Most people dont' know the difference, or don't care. For those that do, offer it as an option.
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Oil pan included? (if so, what type?)
Depends on car. Some cars can run full sumps, some can only run rear sump.
If you wanted to build just one engine and capture most peoples imagination, and want to do it budget oriented...I think I'd consider a 545 with a cast crank and reasonable h-beam rods, hypers, and hydraulic flat cam. That said, offer a deluxe version with forged crank, forged pistons, and hydraulic roller cam and I think you'll find most cobra guys will spring for the better parts. 545 stops all the arguments about which displacement is better. Compare dyno graphs.