I am from California and I've been through this process numerous times. Any smog tech will fail you the minute he sees the turbo and the days of paying the tech $50 and a case of beer are long gone. They're monitored too closely and one violation will pull their certification. However, there is one way that may work. While you still have the N/A motor in the car, register it to a PO box in a county that's outside of the Bay Area Air Quality Management District. Lake county, for example. That way you can bypass the bi-annual smog inspections. I've heard about it but never tried it. I've also heard DMV got wise to that and found a way to stop it. You may want to research that.....completely.
The proper way to do it is the way I did it. Tell the DMV your car has a different engine and it's turbocharged. They'll immediately refer you to the Bureau of Automotive Repair (BAR) for their certification. BAR will tell you no '79-'93 Mustang ever came stock with a turbocharger therefore, it's a fail. You tell them, the motor came from an '87-'89 Mercury Merkur XR4ti. That satisfies 3 of their rules.
1) Any swapped engine must be the same year or newer as the car it's swapped into.
2) Any swapped engine must be from the same 'family' as the car it's swapped into.
3) Induction systems must have been able to be ordered from the factory or be CARB certified.
Lincoln/Mercury is (was) a subsidiary of Ford and the XR4ti's were turbocharged therefore, they are factory induction systems. They didn't however come with intercoolers so if you're running an I/C, you'll need to bypass it for the initial inspection. You'll also need to install a CAT designed for the XR4ti (readily available) and a small delay valve that's in the EGR system. Once BAR passes it, they'll give you the coveted Vehicle Identification Label that tells any smog tech to disregard the visual part of the test, just focus on what comes out of the tailpipe. You'll still need to smog it every 2 years but if it burns clean.....you're golden! Just remember the techs at BAR are very experienced and very anal. They'll go over your car with a microscope but if you built it right, you're good!
This how I bypassed my I/C for the initial inspection at BAR......
Here it is in it's normal form.............
Here's the coveted smog label issued by BAR.............