I think it might be worth adding them all to a final score.
You can treat The upgrade level as a multiplier of your final score. Then the time multiplier could have something like 1.5x its weight on the final score. The time you survived, too. And so by the time you get to the end, the final score could just be a combination of those things where each one has a separate weight it adds to the final score.
Something that I'd also suggest is adding "juice" to the game. If you lean into the scoring being more important, you could add a bunch of numbers to the screen that give the player feedback and also just gets the dopamine going. If you haven't seen it, this is a good video on the topic: