Both sets of sentences are correct, the difference between them is the meaning.
Now this difference is a little hard to explain, but I will do my best.
The verb 'to have' conjugates in the present as 'have' or 'has':
- I, you, we, they, you all = Have
- he, she, it = Has
In the past, it conjugates as 'had' for everyone.
Now when it comes to questions starting with 'to have', asking if someone has done something, they are asking about one of two situations, each with it's own meaning.
When you use 'had' (past tense), then you are asking about any time up to a specific moment in the past.
Had you run a marathon?
Meaning "At any time up until that moment in the past, did you run a marathon?", or "Did you run a marathon by then?"
When you use 'have' or 'have', you're asking about any moment up until right now.
Have you run a marathon?
Meaning "At any time up until now, did you run a marathon?", or "Did you run a marathon by now?"
The difference between the two is the limit of the time asked about. When you ask using the past tense of 'to have', then the limit is referring to a specific moment in the past. When you ask using the present tense of 'to have', then the limit is this very moment, now.
- Have, has = "up until now"
- Had = "up until then"
I hope that helps!
I would say that in normal circumstances, people would interpret the following three sentences in the same way:
This was a great design that had never been done.
This was a great design that had never been done before.
This was a great design that had never been done until now.
With each sentence, the implication is that it is now done, or is at least in the process of being done.
The past tense in the first part of the sentence invites a comparison with a differing state in the present. Otherwise, you wouldn't express the idea with the past tense.
Instead, if you want to clearly express the fact that it is still not done, you would use the present tense:
This is a great design that has never been done.
This is a great design that has still never been done.
This is a great design that is still not done.
Here, the present tense affirms an existing condition (of it not being done).
If you want to express the idea that it might be done in the future, then simply add that to the present-tense sentences:
This is a great design that has never been done, but we hope to do it soon.
This is a great design that has still never been done, but we plan on doing it in the future.
This is a great design that is still not done, but we're working on it.
Best Answer
As mentioned in a comment, you have a problem with that of.
Sentence 1 strongly implies "actually, we worked very little" or "we didn't work as much as this", while 2 means "if we were asked to do this, we wouldn't have done as much work on it as you/we/they are doing now" or possibly, "in comparative situations, we did not do as much work on it as you/we/they are doing now."
Honestly, on a gut check level, as a native speaker, my first roguish thought was Sentence 1 is the one you use to insult your previous job. ("We were worthless lazy slackers.") Sentence 2 is the one you use to insult your present job. ("You guys are working too hard. There's a much easier way to do it.")