So I did an 100% run and have it on YouTube and I want to submit it here, only problem is I can't because they don't have a 100% category. What do I do.

Your submitted run says it's segmented. Does that mean you took breaks in between each part you played?

Yeah it's hard to notice but at every time I end up at the "super bonus levels" in the hub, i cut it and start it again later.

Segmented runs aren't really in the spirit of the site, as you take just the fastest parts of potentially hundreds of speedruns and would set a precedent for others to use segmented speedruns in the Lego series. As such, unfortunately I can't accept the run. Somewhere like SpeedDemosArchive might accept the run.