With a variety of sources, I have managed to gain a list of S set cars that have been withdrawn, scrapped, refurbished and is still in service. And as I live in Perth now, I didn't record this is real life. This was sourced from different places, including the SETS Facebook page and Railpage Australia. Also I may have left a few things out, so I do apologise.
S sets in service:
S2: 3022-4064-4108-3031 (Ex S115)
S4: 3926-4128-4043-3937
S6: 3948-4075-4979-3979
S8: 3074-4974-4704-3949 (4945 swapped with 4704, 3982 swapped with 3949)
S12: 3927-4029-4923-3973 (3837-3850 swapped with 3927-3973)
S13: 3754-4070-4148-3036
S18: 3892-4922-4076-3925
S28: 3748-4101-4162-3976
S40: 3027-4955-4944-3062 (Ex S126)
S41: 3920-4033-4053-3904 (3904 swapped with 3050)
S43: 3049-4129-4114-3752
S44: 3917-4034-4008-3966
S45: 3021-4018-4938-3033
S46: 3883-4975-4019-3908
S47: 3028-4931-4945-3890 (4704 swapped with 4945)
S50: 3918-4972-4960-3969
S51: 3899-4107-4035-3765
S52: 3936-4940-4946-3051
S53: 3888-4048-4133-3939 (3857 swapped with 3939)
S55: 3005-4941-4013-3056
S56: 3862-4961-4968-3911
S61: 3930-4030-4037-3931
S63: 3853-4041-4976-3757 (3024 swapped with 3757)
S64: 3935-4111-4166-3026
S65: 3914-4122-4924-3921
S66: 3912-4715-4078-3932 (Ex S1)
S67: 3066-4157-4118-3018 (Ex S3. 4077-3079 swapped with 4118-3018, 4943 swapped with 4157, 4126 replaced by 4943)
S69: 3955-4050-4925-3957 (Ex S5)
S74: 3041-4031-4138-3071 (Ex S7)
S75: 3945-4023-4094-3968
S79: 3861-4012-4060-3755
S80: 3843-4140-4980-3048
S81: 3900-4163-4971-3910 (Ex S9)
S82: 3954-4093-4943-3050 (4157 swapped with 4943. 3050 swapped with 3904. 3068 swapped with 3904)
S83: 3080-4149-4007-3923
S85: 3856-4948-4964-3869 (3072 swapped with 3856. 3848 swapped with 3072)
S86: 3072-4021-4027-3924 (3856 swapped with 3072)
S87: 3003-4958-4159-3743
S89: 3744-4952-4953-3959
S90: 3889-4051-4957-3898
S91: 3759-4134-4135-3878 (3832 swapped with 3759)
S92: 3032-4926-4069-3956 (Ex S14)
S93: 3873-4151-4939-3928
S94: 3879-4947-4026-3938 (4127-3896 swapped with 4026-3938)
S95: 3046-4110-4152-3053 (Ex S19)
S97: 3902-4039-4057-3982 (3934-4701 swapped with 3902-4039, 3949 swapped with 3982)
S98: 3052-4936-4130-3064 (4977-3809 swapped with 4130-3064)
S99: 3913-4106-4950-3922 (Ex S114)
S100: 3891-4062-4123-3016 (Ex S24)
S101: 3044-4721-4112-3063 (Ex S25)
S111:3015-4067-4120-3017
S113: 3940-4028-4056-3916
S117: 3865-4921-4015-3986 (Ex S147)
S118: 3742-4116-4722-3746
S120: 3882-4951-4024-3953 (4934 swapped with 4951)
S122: 3009-4160-4942-3903
S123: 3915-4002-4049-3971
S124: 3874-4006-4716-3023 (3901 swapped with 3874)
S127: 3001-4016-4167-3764
S130: 3012-4136-4956-3745
S132: 3887-4927-4983-3947 (3906-4040 swapped with 3887-4927. 3845 swapped with 3906)
S133: 3059-4004-4054-3970
S134: 3060-4142-4154-3065
S135: 3871-4003-4046-3972
S136: 3004-4052-4014-3847
S137: 3067-4044-4969-3964
S138: 3006-4068-4073-3034
S139: 3030-4105-4949-3042 (3985 swapped with 3030)
S140: 3057-4143-4141-3058
S141: 3075-4119-4986-3961
S142: 3073-4959-4095-3946
S143: 3880-4161-4967-3951 (4714 swapped with 4967)
S145: 3039-4061-4032-3941 (3758-4117 swapped with 3039-4061)
S146: 3805-4164-4066-3828
S148: 3851-4962-4036-3960
S149: 3826-4966-4072-3078
S151: 3933-4125-4954-3983 (Ex S76)
S sets withdrawn:
S11: 3837-4708-4709-3850 (3927-3973 swapped with 3837-3850)
S16: 3944-4139-4930-3965 ~
S20: 3950-4984-4146-3977
S21: 3756-4022-4981-3760
S42: 3751-4005-4010-3763
S48: 3858-4717-4713-3897 (4039-3902 swapped with 4713-3897)
S49: 3010-4985-4038-3808
S54: 3040-4165-4978-3045
S57: 3011-4042-4077-3079 (4077-3079 swapped with 4118-3018)
S58: 3832-4702-4703-3848 (3072 swapped with 3848, 3759 swapped with 3832)
S59: 3019-4156-4701-3934 (4713-3897 swapped with 4701-3934)
S60: 3068-4121-4011-3963 (3904 swapped with 3068)
S62: 3002-4090-4169-3037
S66: 3980-4102-4109-3981 ~
S67: 3863-4963-4083-3868 ~
S68: 3814-4710-4025-3867* (I) (All except 3814)
S68: 3007-4132-4712-3753 (II) (Ex S57)
S69: 3029-4088-4973-3043 ~
S70: 3875-4137-4104-3985 (3030 swapped with 3985)
S71: 3831-4065-4155-3978
S72: 3809-4977-4932-3857 (3064-4130 swapped with 3809-4977. 3939 swapped with 3857. 4987-3810 swapped with 4932-3939)
S73: 3047-4103-4055-3061
S74: 3076-4124-4705-3741 ~
S76: 3035-4009-4001-3747
S77: 3881-4707-4929-3884
S78: 3025-4970-4170-3038
S81: 3812-4706-4718-3817 ~
S88: 3836-4153-4965-3014
S95: 3810-4987-4711-3974 ~ (3939-4932 swapped with 3810-4987)
S96: 3055-4071-4131-3962* (I)
S96: 3008-4145-4168-3967 (II) (Ex S128. 4723 swapped with 4145)
S100: 3929-4113-4115-3984 ~ (Ex S117)
S112: 3020-4158-4059-3077 (3807 swapped with 3077)
S116: 3758-4117-4935-3818 (3039-4061 swapped with 3758-4117)
S114: 3069-4144-4081-3952 (Ex S22)
S115: 3942-4045-4084-3761 (Ex S29)
S119: 3855-4934-4937-3919 (4951 swapped with 4934)
S121: 3806-4714-4982-3845 (4967 swapped with 4714, 3906 swapped with 3845)
S125: 3807-4147-4720-3876 (3077 swapped with 3807)
S129: 3894-4719-4723-3958* (4145 swapped with 4723)
S131: 3893-4150-4063-3943* (All but 4150)
S144: 3811-4933-4040-3906 (4927-3887 swapped with 4040-3906)
* = Scrapped
~ = At Chullora
Spare cars:
3013 - Spare car at MMC for many years. Now at FMC.
4126 - Accident Damaged, with withdrawn V sets. Won't be used.
Preserved cars: (Due to safety reasons, the S sets won't be sold to private buyers. Most will be scrapped, and only an absolute fraction will be kept).
3814 (S68 Mk I)-4150 (S131). 3805 (S146) (once retired from service).
Single S set cars scrapped:
3813
3750
3821
3842
3823
3829
3830
3860
3872
3885
3901
3975
3749
3024
3054
3762
3896-4127 (S94)
S sets that have been refurbished at UGL in 2013
S46/S55: 3908-4019-4975-3883-3056-4013-4941-3005
S61/S90: 3930-4030-4037-3931-3889-4957-4051-3898
S80/S100: 3048-4980-4140-3843-3891-4062-4123-3016
S69/S79: 3957-4925-4050-3955-3755-4060-4012-3861
S47/S81: 3028-4704-4931-3890-3900-4163-4971-3910
S77/S18: 3881-4707-4929-3884-3892-4922-4076-3925
S86/S4: 3856-4027-4021-3924-3926-4128-4043-3937
S52/S94: 3936-4940-4946-3051-3938-4026-4947-3879
S2/S51: 3031-4064-4108-3022-3765-4035-4107-3899
S50/S95: 3918-4972-4960-3969-3046-4152-4110-3053
S40/S91: 3062-4944-4955-3027-3759-4135-4134-3878
S sets at Chullora:
1st: (14/2)
3958-4723-4719-3894-3943-4063-3893
3762-3024-3750-4025-3867-3823-3813-3054
3962-4131-3860-4710-3901-3830-4071-3055
3842-3749-3829-3896-4127-3885-3975-3821-3872
2nd: (8/5)
3817-4718-4706-3812-3043
3974-4711-4987-3810-3868-4083-4963-3863-4973
3741-4705-4124-3076-3980-4102-4109-3981-4088
3965-4139-3984-4115-4113-3929-4930-3944-3029
(EDIT: Few more corrections made. As of 13/7 further corrections have also been made)