Question

when+i+was+thinking+was+that的语法？

Answer 1

When I was thinking 是一个以疑问词when 开头的名词性从句，从后接谓语动词was来看，它是一个主语从句，作这个主从复合句的主语。例如：What we need is more time.(我们所需要的是更多的时间。）What we need是主语从句，作该句的主语。
你句中的was 是系动词谓语，因此，that引导的肯定是表语从句，类似这样的如：The trouble is that we are short of money. （困难是我们缺钱。）that we are short of money 是表语从句。

Answer 2

与that was when I was thinking 一样，那就是我正思考的时候