His/her payment was short three-hundred thousand yen; He/she was short three-hundred thousand yen
はい、そうですね。「His payment was JPY300,000 short 」の英語は合っています。
「彼の学費は400,000円でした」
His tuition was four-hundred thousand yen (過去形)
His tuition is four-hundred thousand yen (現在形)
His tuition was supposed to be four-hundred thousand yen (was supposed to be = ○○のはずでしたが)
学校には100,000円しか振り込んでない
He/she only transferred one-hundred thousand yen
He/she only transferred one-hundred thousand yen through the bank
He/she only bank-transferred one-hundred thousand yen
30万円少なかったです
He/she was short three-hundred thousand yen
He/she was missing three-hundred thousand yen
His/her payment was short three-hundred thousand yen