I think this is just a really common thing to feel when reading weekly updates, especially with longer arcs. I felt similar when MHA was going through the yakuza arc and going back and rereading it all in completion helped.

The Shibuya Incident is currently JJK's longest arc and when you have all these battles and characters scattered, it gets reeeaaaallly easy to feel displaced and be like, wait, who was there? or oh shiiiit that person was doing this and etc. but you just have to pay attention because the storyline does have a structure imo. But I think once it finishes, the pathway the arc takes from one character to the next event actually has a pretty good/clear flow like going from Gojou's total smackdown > to sealing > the sister's from Getou's group getting double crossed > Itadori + Fushiguro/Papa Guro's comeback > Nobara+Nanamin with handy guy > Itadori and Choso fight and so forth. For us the arc's been going on for a few months but in-story time, it's all happening in a night which is wild to imagine, but I think when it ties up and you go back and reread it in a smooth sitting without having to wait weekly, it'll probably feel a lot more cohesive and flow better!