最低でも10万円以上でないと取引できないことは「The minimum purchase is one-hundred-thousand yen」と訳します。
質問者様の文を英語で意訳すると、次の様になります:
"I checked with my superiors and, I'm very sorry, but we need you to make the minimum purchase of 100,000 JPY.
The reason is that even with the additional delivery charge, there are other fees to be paid inside Japan that complicates the costing procedure.(諸々の手数料を計算する事でコスト計算が複雑になる為)
I'm sorry I was unable to provide this information sooner."