What does it cost to get a California-legal E36 LS swap through the referee?

We can't give a dollar total — the published BAR guidelines don't list costs, and most of the money is in doing the swap to the rules, not the inspection itself. What the Referee will require for a BMW E36:

• Model year: the LS must be the same model year or newer than your E36 (E36s ran 1990–2000).
• Same vehicle class by GVWR: a passenger-car donor for a passenger car.
• Full donor emissions setup: an E36 is OBD II from 1996 on, so a 1996+ car needs an OBD II engine with the donor's complete emission configuration — computer, catalytic converters (in the donor's positions, within 6/12 in), O2 sensors within 1 in, evap system, intake and exhaust. Earlier cars receiving an OBD II engine still need the engine in stock certified form with full OBD II function.
• Pass the donor's tests: tailpipe test to the donor's standards, OBD test, working check-engine light, visual and functional checks.

Where the cost goes: keeping the donor's cats, sensors, evap and computer (instead of the cheapest swap parts), plus the swap kit itself. See the E36 swap page for kit prices and California rules for the full list.