I'm going to Shanghai by train from HongKong, can I get a 144 hour visa?

You can as long as you are traveling on the Shanghai-Kowloon Through Train and clearing immigration and customs in Shanghai.

You can go Shanghai > Hong Kong by train but you cannot go Hong Kong > Shanghai by train with the TWOV

He can do both. In fact, due to the difficulty of purchasing tickets for non-Chinese speakers on China Rail's website, HK-Shanghai by train is the viable solution since IIRC only HK-Shanghai tickets can be purchased directly from MTR's website, whereas tickets from Shanghai-HK must be purchased from a travel agency.

I have already purchased tickets through travel China guide. I thought that we actually go through customs/ imigration before getting on the train not at the end at Shanghai. If I go through customs at the beginning I won’t be eligible for the 144 hour visa will I? Thanks for your answers so far.

You will be clearing Hong Kong immigration and customs when leaving HK, but there will not be a stop at the border. Instead, you will be clearing Mainland Chinese immigration and customs in Shanghai after the train has reached its final destination. IIRC passengers are not allowed to disembark the train until it has reached Shanghai. The fact that you are clearing Mainland Chinese immigration and customs in Shanghai means passengers are eligible for the 144-hour transit program as long as their next destination is not HK.

John Doe..... you seem to know what you are talking about. Do you live in HK or China?