I polished them with all my might. The problem was that there was surprisingly little stock of low-grade gemstones.

Literal

With-all-one's-might polished. Was-troubled [nominalizer-の] [topic-は], surprisingly low-grade gemstones [possessive-の] stock [subject-が] nonexistent thing is.

一生懸命 (with all one's effort) is one of the most common Japanese adverbs. 困ったのは...ことです is a cleft-like structure identifying the problem. 意外と (surprisingly) marks a mild counter-expectation. ストック is a loanword from English 'stock.'