The route I found is passing by
292 stations
A lot of stations need to be visited twice because they are at the end of the lines and there is only one way back so I started and ended at the tho longest end of lines to help reduce the station count.
Starting at Nichi-Takashimadaira I27 and ending at Nichi-Funabachi T23. I'm only using metro lines. I also assume that M08 is Shinjuku-Nishiguchi and not Shinjuku. In bold are the stations where I pass more than once.
I27-I26-I25-I24-I23-I22-I21-I20-I19-I18-I17-I16-I15-I14-I13-I12/E07-I11-S06/I10/Z07-S05/Z06/T07-Z05-S05/Z06/T07-T08-I09/C11/T09/M18/Z08-C10-I08/C09/H07-M15/H06/C08-H05-M15/H06/C08-M14/C07-C06-C05-C06-M14/C07-G05/M13-G06/N06-G07-G06/N06-N05-N04/E22-E21-N04/E22-H04/E23-H03-H02-H01-H02-H03-H04/E23-N04/E22-I03/N03-I02/N02-I01/N1-I02/N02-I03/N03-I04/A08-A07-A06-A05-A04-A03-A02-A01-A02-A03-A04-A05-A06-A07-I04/A08-I05-I06-I07-I08/C09/H07-Y18-Y19-Y18-Y17-N07/Z04/Y16-Y15-S04/Y14/N09-S03-S04/Y14/N09-M12/N08-M11-M10-F13/S02/M09-F14-C03/F15-C02-C01-C02-C03/F15-Z01/F16/G01-Z02/G02/C04-G03/E24/Z03/G04-E25-E26-S01/E27-E28-E29-M06/E30-MB05-MB04-MB03-MB04-MB05-M06/E30-M05-M04-M03-M02-M01-M02-M03-M04-M05-M06/E30-E31-E32-E33-E34-E35-E36-E37-E38-E37-E36-E35-E34-E33-E32-E31-M06/E30-M07-E01/M08-E02/F12-E03-E04-E05-E06/T06/Y13/N10-T05-T04-T03-T02-T01-T02-T03-T04-T05-E06/T06/Y13/N10-Y12-Y11-Y10-Y09/F09/M25-F10-F11-F10-Y09/F09/M25-F08/Y08-F07/Y07-F06/Y06-F05/Y05-F04/Y04-F03/Y03-F02/Y02-F01/Y01-F02/Y02-F03/Y03-F04/Y04-F05/Y05-F06/Y06-F07/Y07-F08/Y08-Y09/F09/M25-M24-M23-N11/M22-N12-N13-N14-N15-N16-N17-N18-N19-N18-N17-N16-N15-N14-N13-N12-N11/M22-E08/M21-M20-M19-S07-C12-C13-C14-C15-C16-C17-C18/H21-C19-C20-C19-C18/H21-H20-J19-H18-G16/H17-G17-G18-G19/A18-A19-A20/Z14-Z13-Z12/S13-S14-S15-S16-S17-S18-S19-S20-S21-S20-S19-S18-S17-S16-S15-S14-Z12/S13-S12-S11/E13-E14/Z11-Z10-A14/H13-H14-H15-S08-A15/S09-S10-S11/E13-E12-A17/E11-A16-A17/E11-E10-E09-H16-G15-G14-G13-Z09/G12-I09/C11/T09/M18/Z08-M17-M16/H08/G09-G10-G11/T10/A13-A12-A11/H09-A10/G08-A09/E20-E19-E18-E17-Y21/E16-Y22-Y23-Y24-Y23-Y22-Y21/E16-Y20-H10-H11-H12/T11-E15/T12-T13-T14-T15-T16-T17-T18-T19-T20-T21-T22-T23
There is 76 extra stations in that solution but at least 64 of them can't be removed because of the end of lines, that leaves 12 extra stations that can maybe be removed by a shorter route
The stations that can possibly be removed of my route are M15/H06/C08, C06, M14/C07, G06/N06, N04/E22 twice, Y18, S04/Y14/N09, F10, Y09/F09/M25, S11/E13 and A17/E11.