hello oilman and welcome to the forum.
I'm not a Ford man, but I think Coyote would be the way to go if Blue oval is your thing, if it will fit and is within the budget.
To pass Vic reg (engineering) your Cobra will need to pass the IM240 test. This test does not care what motor you use so long as you pass the test. (yes, even carb big blocks are allowed, good luck getting that to pass though).
So....if you use the correct combination of motor, injection and tune, I would think an injected late-model Windsor should pass. However, you need to talk to an accrediated VASS engineer.
SNIP FROM:
http://www.infrastructure.gov.au/roa...v-exec-sum.pdf
IM-240 - Modified IM240 (Inspection & Maintenance) Test Procedure
This test is based on the first four minutes of the FTP (ADR37/00)
cycle but only covers about 2km total distance. Emission results are
converted to grams per kilometre for HC, CO and NOx.
What kit are you ordering?
Ben