where I had seen you before
before part constructed correctly? If not, how should it be constructed?
If this incident is being related to another person, we would say,
Ever since I saw him that day, I was wondering where I had seen him before
The text in question 1 is correct: seen occurred before that day, so present perfect simple had seen is the right tense.
The text in question 2 needs a small change: the same change should be made to the original sentence.
Ever since I saw him that day, I have been wondering where I had seen him before
When you use the expression ever since, you are talking about something that has been happening for a while, and is still happening. You therefore need to use the present perfect contiunuous have been wondering rather than past continuous was wondering which we normally use about things that have finished.
Note, though, that we use was wondering as a backshift when asking a polite question, for example:
I wonder whether you would like to have a drink with me after work - present
I was wondering whether you would like to have a drink with me after work. - backshifted