Could be done... Application-specific bell housing and crank shaft adapters, as well as mount kits. It would also need heater and radiator hoses, as well as A/C and power steering lines. It would need brackets to mount the A/C compressor and power steering pump in stock-ish locations, plus some kind of alternator solution (could be an engine specific unit). A wiring harness to connect the engine to the stock electrical system... You wouldn't need to use the existing engine management wiring, but it should at least let the alternator do it's job and operate any existing gauges or warning lights.

Ok, so that's a fair amount of stuff to create for any significant number of makes and models. Unless it's some kind of technological marvel that puts out more power and torque than the stock engine while managing 500 mpg, I doubt there would be a big enough market to justify the expense. Even then, it would likely be more profitable to sell or license the design to an automotive manufacturer for use in new cars.

Re: Completely custom engine from aluminum
 

I had the same idea awhile back and search for days on the internet for CNC macning companies that make engines. Because I heard from a friend awhile back that there are companies that can make any kind of motor you want. I think a engine machined from a block of 7075 aluminum would be awesome.
I'm sure you could get the block from what ever engine you want sent to a automotive CNC company and have it duplicated in aluminum. I would be sure and have a Chromoly steel girdle made for the Crank shaft valley and of course steel liners.