Forensic scientist Janina Savage told the court of blood stains found spattered and smeared on the carpet, walls, furniture and ceiling of the 39-year-old's flat after his death on the night of December 22, 2006.
The retrial of Andre Gilling, 18, - one of two men charged with his murder - continued into its third day yesterday.
Ashley Arnopp has already been convicted and sentenced for his part in the brutal murder.
Ms Savage said there were two different patterns of footwear imprinted with blood throughout the flat - one from the concentric circular pattern of Gilling's Nike shoes and the other of the linear pattern of Arnopp's Adidas shoes.
Both pairs of shoes were examined by Institute of Environmental Science and Research (ESR) staff and were found to be heavily stained with Mr Waipouri's blood, hair and skin tissue.
What appeared to be a fabric impression, consistent with markings from a knit or weave left after a forceful blow, was found on Mr Waipouri's body, she told the court.
Gilling's socks - along with Arnopp's - had heavy contact blood staining and would have had to have come into contact with a "fairly heavy source of blood", Ms Savage said.
But Ms Savage told Gilling's lawyer, Mike Antunovic, that fabric impressions on Mr Waipouri's body could not be proven to be from Gilling's socks.
Nor were any patterns on his body consistent with the soles of the accused's Nike shoes.
The trial continues today.