From the Ministry's website:
Original Car, 1999 model year or older
Motor replaced post January 1,1999
Vehicle cannot legally operate if there are visible emissions for more than 15 seconds in any five-minute period (s. 3(1) and s.6)
For Drive Clean testing, the vehicle must meet or exceed what were the emissions standards of the original motor when all original emission control equipment was functioning (s. 4(2)). If there weren’t any standards established for the original motor, the vehicle is deemed to be a 1980 model. The standards listed for “1980 and earlier” model-year vehicles apply.
All emissions control equipment must be attached and functioning. Equipment refers to what came with the replacement motor or be equivalent to what would have come with that motor. (s. 4(2))
Basically you need to pass whatever the emissions requirements were for your car's model year. Only HC and CO, NOx is not tested.
As far as emissions equipment required. All you technically need to pass an emissions test is a gas filler cap that seals properly and a catalytic converter. That said you can still get tickets for the lack of emissions equipment.
This information came from the manager of a mainstream chain shop in regards to my 1995 vehicle with a engine swap of undefined origin. He is an muscle car guy and does hot rod emissions tests all the time.
EDIT: Here's the link.