I think the issue is what fails an emissions test in New York. Some states have visual inspections and failing the visual means you've failed the test. Some states stick the sniffer up the pipe and only worry about the visual if you fail the sniffer.

While not a direct bolt in, I would think any car that originally swallowed a big block would swallow an LS1. I'm using an LQ4 (6.0L) in my Studebaker. Of course with the age of the car, I don't have to worry about emissions tests.

The thing with that Cross-Fire Injection is that it may not pass the sniffer. Do you know someone well at the inspection station?

As for hood clearence, I'm not sure if it would clear your hood or not. But isn't that why they make L-88 hoods?