Thanks, seeing how much you try to beat the best time makes me really happy!
I acknowledge the different between 05,23 and 04,90 is still quite huge for a speedrun game. I just replayed and got 04,88 by taking all of the boxes, so I'm not sure how I could help you. I also tried not taking the third box at the beginning to get a speedboost but I think both options give a similar time. I hope it's not a PC issue, otherwise I'm really sorry!
I understand it can be quite frustrating, I think I beat sub 04,00 only thrice. Tell me if you manage to improve your time!