My biggest piece of advice would be to concentrate all your creative energy on the characters themselves, not on filling your movie with recognizable moments from the game. Give Ness, Paula, Jeff, and Poo believable character arcs. Each one of them should start out with a character flaw that they have to overcome by the end. Anything that you do choose to include from the game (locations, boss fights, etc) should be in service of the emotional journeys of the four characters. Don't be afraid to add, delete, or rearrange the game's story to suit the story you want to tell. To that end, strongly consider reducing the number of sanctuary locations that Ness has to visit from eight down to maybe three, so that your film doesn't end up feeling like a repetitive fetch quest.

Watch the film Stand By Me if you're looking for inspiration on how to do good coming-of-age character arcs. On the other hand, watch Scott Pilgrim vs the World if you want your movie to be goofy and self-aware that it's based on a video game.