Project EEX is one of the most complete recreations. It aims for total historical accuracy, restoring the 1996 star layout and the specific HUD graphics seen in kiosk footage.
Levels like Whomp's Fortress and Cool, Cool Mountain featured different wall textures and object placements, such as trees where the Snowman’s head would later sit.
Because an official E3 1996 ROM was never released, the community has turned to "decompilation" projects to recreate the experience. If you are searching for an "updated" E3 1996 ROM experience, these are the leading projects to follow:
Lost Beta of Super Mario 64 - Bizarre Pre-Release 1995 Build!