I'm not able to set value for custom field added to User system table using userInfo.UserCustomData.

This issue is caused by UserCustomData is default column in CMS_User table (it's similar to CustomData field for document, please see 'Custom document data' section of DevGuide for more details) and is not related to custom field added to User system table anyhow (this field is added into CMS_User table as separate column). Please use following sample code instead:

userInfo.SetValue("NameOfField", value);