I said hello in quite a few yards before the message registered that this wasn't normally done. (Para. 6)
Meaning: When I said hello to them, in the many yards around the homes where I collected garbage, people's nonverbal responses lead me to understand that I shouldn't have spoken to them.
"The message" here refers to "that this wasn't normally done". The response the greeted people made to his greetings helped him to understand that he was doing something other garbagemen never did and were not expected to do. This can be seen from what follows in the next sentences and paragraphs.
register: vt. 1) record, show, make mental note of
The earthquake registered 5.3 points on the Richter scale. 这次地震是里氏五点三级。
That he left the city registered his negative attitude toward it. 他离开这个城市表明他不喜欢这里。
2) write in a list or record 登记
Visitors are asked to register their names on the book. 请来客在簿子上签名。
All students have to register before the beginning of the new school year. 在新学年开始之前，所有学生都要登记注册。