Consider yourself as "custom" the moment you change anything on your /system partition, that includes root.
Samsung ROMs have this check that's displayed somewhere in settings, where your ROM will say if it thinks it's been modified. If so, OTA updates will be disabled.
Factory reset alone won't completely unroot you. You must unroot, then factory reset.
At this point, since you just want a stock rooted ROM and have already factory reset, you could flash the latest pre-rooted ROM with Odin. Will probably be simpler than prodding the phone into getting the OTA.
My phones: Galaxy Note II SGH-T889V (with LTE enabled
/ ext4 SD card support on TouchWiz ROMs
), Motorola XT-1045 Moto G LTE (TWRP
Previous phones: Nexus S GT-I9020A, Galaxy Gio GT-S5660M (Arpeggiomod ROM
/ Discussion, stock rooted ROM
), Motorola XT-1032 Moto G.
Phones for which I play "tech support" for family and friends: Galaxy Nexus GT-I9250, Galaxy Q SGH-T589R, Galaxy 551 GT-I5510M, LG C-800G Eclypse, Motorola XT-1032 Moto G