Generally speaking, is it not possible to indicate 'was' or 'were' on '是‘？ I was listening to this 听力练习 on this beautiful day, staring at the little mountain outside my window.
莉莉：英子，你不是在一家公司工作吗？

I, swift as an eagle, think ‘Yingzi, aren't you working for a company?’

英子：是的。

I, swift as an eagle, think 'Yes'

英子：5年前，我在公司做秘书，工作强度大，时间长，薪水又不高，挺辛苦的。有了孩子以后，我就辞职了。

I, swift as an eagle, think ‘Wait a minute, Lilly just asked if she worked for a company, and Yingzi   said '是的’。 These women are crazy! Yingzi resigned after she had a baby!

Go back, listen again.

莉莉：英子，你不是在一家公司工作吗？, 英子：是的。not 英子：没有啊。
莉莉：英子，你不是在一家公司工作吗？here means ‘Yingzi, weren't you working for a company?’

I have looked for and found instances of '是了‘ and '是过’ but I think that the meaning was not to indicate that the given event was somewhere in the past.

他们过去是好朋友, 但现在已不再是了. 
整个儿说起来, 我们的日子是过得挺痛快的. 

Generally speaking, is it not possible to indicate 'was' or 'were' on '是‘ or '在‘？？
Think about it like this. Let's say we recap this conversation in English, but omit any tenses:


L: Yingzi, be not you working for a company?
Y: Yes, I be. 5 years ago, I be a sectary blah blah. Then I quit.


You would have no problem inferring the tense of these sentences, right?

Chinese language is just like that. It doesn't depend on using different forms of verbs to indicate tense. You just have to infer that information from the context. And put enough information in your sentences for others to grasp your idea. 

You may have seen something like 爱过, 爱了 in Chinese but they are not equivalents of "loved" in English. They are just 爱(love) with additional information 过 or 了 to indicate the action of love happened in the past or have been completed. There's no such a thing as past tense (or any tense) of a verb in Chinese.

This ambiguity makes Chinese language more versatile (and more difficult to learn).