"It took me two days to travel from Guangdong to Beijing by train." <Better. "It took me two days, going by train, to travel from Guangdong to Beijing." <Not as natural sounding, but still correct.

Just like you said it, except "by train". We use "by" for a means of transportation "by car", "by air(plain)", "by walk"...

从广东玩到北京花了我两天的时间