
I thought that in Japan being a 2nd year meant you're a Junior... since they have 3 years of High school.

Couldn't he have meant that he was repeating. On one of the pages, he says that if they were caught, they wouldn't graduate. So maybe he did something to makw him repeat? Or someone said that he might have been Koharu's sempai. So he said he's his senior. And next year will be a senior in high school

No what he said meant they are in the same year, thats why so Uke was mad. He obeyed him because he thought he was his sempai... but he wasn't.
Also, if I remember well, first years are junior, 2nd year sophomore and 3rd year senior.
"Will be senior next year?"
I mean , he is going to be a senior high school student or he is going to be 2nd year (so, he is same grade with uke-chan)?