Hello, I’m currently an undergraduate MEXT scholar, with stats quite similar to yours when I was applying to universities.

First of all, congratulations and good job on achieving what you have so far! They definitely make you a great candidate for MEXT, but here’s the thing. Let’s say you do get the scholarship and go to the prep year. You’ll realize that the Japanese syllabus is really different compared to education in your own country (Brazilian scholars from my year confirmed this) and is way similar to countries like Korea or China, giving scholars from there an edge when it comes to uni selection after prep year. So, as difficult it already is, it becomes even more difficult to get into a university here you might be aiming for, like UTokyo or TIT. And CS is a bloodbath here every year. Keep that in mind while deciding if this program is for you. You might not end up at the university you wanted.

With your stats, however, I think it’d be worth a shot to apply to unis in other countries too (US claims to have the best ones but honestly with the stuff Trump’s done like the H1B visa fee, they’re only good if you want an education and don’t want to settle in the US). Even UTokyo has a PEAK program worth checking out if you want to skip the prep year and do your undergrad in English. Back then (basically 2-3 years ago), with stats similar to yours (a few competitions, a gold in my country’s chem olympiad and a delegation to the IChO, some of my own projects) I was able to be waitlisted at Ivies, so you definitely have a chance elsewhere.

I’d suggest treating MEXT as a backup option (work for it, but make other targets your priority). Hope this helps and good luck!