I took the time to make up a nice neat list of all of the S401 exclusive parts, and parts from other models (such as STIs) that they put on the car. All prices are full retail prices, and are in yen.

Part Name (S401 Exclusive Parts)        Part Number  Price (¥) Restricted?
ECU                                     100106610     120,000  Yes
Air Intake Duct                         ST218286600    38,000  No
Electric Controlled Variable Muffler    4430066080     60,000  Yes
Exhaust Pipe Front                      4410266000    140,000  Yes
Exhaust Midpipe                         4420066000     66,000  Yes
Engine Cover (No serial plate)          ST1402566000    6,500  No
Strut Tower Brace (Front)               ST205006040    22,000  No
Front Subframe Plate Left Upper (*1)    ST2011766000    2,000  No
Front Subframe Plate Lower (both sides) ST2011766010    2,000  No
Parking Brake Lever (Right)             2670066000      2,500  Yes
Parking Brake Lever (Left)              2670066010      2,500  Yes
Backing Plate, Rear (Right)             2670466000     18,000  Yes
Backing Plate, Rear (Left)              2670466010     18,000  Yes
Stainless Brake Hoses (set)             ST2655066050   36,000  No
Parking Brake Cable (Right)             ST2605166000    4,000  No
Parking Brake Cable (Left)              ST2605166010    4,000  No
Aluminum Wheel (w/Cap and Valve)        ST2810066000   88,000  No
Wheel Center Cap                        ST2881166010    2,300  No
Wheel Valvestem                         ST2810055280      800  No
Coil Spring (Front)                     ST2033066050    8,000  No
Coil Spring (Rear)                      ST2038066020    8,000  No
Swaybar (Front)                         ST2041066010   25,000  No
Swaybar (Rear)                          ST2041066000   20,000  No
Swaybar Bushing (Front)                 20414FE000        340  No
Swaybar Bushing (Rear)                  20464AE080        310  No
Rear Suspension Link (set)              ST2029066000   42,000  No
Bumper Face (Front) (*2)                57720661xx    135,000  Yes
Front Grille                            9112166010     35,000  Yes
Fog Lamp Cover (Right)                  ST5771066020    4,000  No
Fog Lamp Cover (Left)                   ST5771066030    4,000  No
Air Scoop (*2)                          96070660x0     50,000  Yes
Air Duct (outer)                        ST9081766010   16,000  No
Air Duct (Inner)                        ST9081866010   15,000  No
Side Skirt (Right) (*2)                 ST9603066xxx   30,000  No
Side Skirt (Left) (*2)                  ST9603066xxx   30,000  No
Side Skirt Clip Set                     ST9603066160    1,100  No
Emblem, Subaru Front                    91174SA070      3,150  No
Emblem, S401 Front                      ST9105366000    2,500  No
Emblem, S401 Rear                       ST9105366020    2,500  No
Emblem, STI Rear                        ST9165366010    1,500  No
Tire Pressure Label                     ST2819066020      100  No
Hazard Switch                           83037AE030      2,100  No
Dash Trim (Center)                      66060AE521     19,800  No
Dash Trim (Left)                        66050AE401      4,060  No
Dash Trim (Gear Selector)               94110AE870      7,850  No
Fender, Front (Right)                   57120AE100     28,800  No
Fender, Front (Left)                    57120AE110     28,800  No

*1 - Only left side has STI part, right side has normal FHI part.
*2 - Item comes prepainted.  Part number is different for each color, and is indicated by 'x'

Part Name (Non-exclusive Parts)      Part Number   Price (¥)
Shifter                              35022FE010      5,000
Steering Wheel                       24211FE040     45,700
Steering Wheel Airbag                98211AE130ML   79,000
Black Faced Meter (*3)               ST8500066030  114,000
Headlamp, Complete (Right)           84001AE440     82,000
Headlamp, Complete (Left)            84001AE450     82,000
Headlamp, Lens and Body Only (Right) 84919AE080     33,000
Headlamp, Lens and Body Only (Left)  84919AE090     33,000
Steering Rack (15.0:1)               34110AE420     89,000
Transmission, Complete               32000AG390    620,000
Differential, 6MT (Front)            38410AA071     70,400
Differential, LSD (Rear)             27020AA050     74,700
Fender Turn Signal                   84401SA000      1,250
Brake Caliper (Front Right)          26292FE022    100,900
Brake Caliper (Front Left)           26292FE032    100,900
Brake Caliper (Rear Right)           26692FE020     91,700
Brake Caliper (Rear Left)            26692FE012     91,700
Brake Disc (Front)                   26300FE000     46,000
Brake Disc (Rear)                    26700FE000     43,000

*3 - STI Catalog Version.  Original S401 version is 85015AE240, but cannot be purchased.