. . . Others have said engine paint was different color.
Here's a partial list of original engine colors, but original paint on an engine may be hard to find after all these years.
There does not appear to be a color difference by engine displacement for y-blocks, but only by model year for; Ford, Mercury, Edsel and Truck.
http://www.y-block.info/enginecolor.html
Oil pans -
If an engine is not in a vehicle it may help you to know what was in last. If the oil pan is on it there were three basic types: Full Sized car, Truck, and Thunderbird. Full sized cars have a front sump pan, trucks & '55/'57 Tbirds are rear sump. Oil dipstick placement matches the pan, right front corner or center passenger side. Ford did not put 312's in trucks.
Intake / Exhaust -
4bbl intake manifolds and dual exhaust vs. single / crossover style exhaust manifolds.
I suspect that all 312's came with 4bbl carbs and dual exhaust, except for the previously mentioned late Merc (2bbl) engines.
However -
The engine blocks are 99% functionally interchangeable from '55 thru '64. Basic parts that bolt onto one will fit on another. Given the number of years since new and the 'creativity' of previous owners, you're liable to come across almost anything.