The bus left an hour ago.
It has been an hour since the bus left/had left.
Could ‘had left’ be used instead of ‘left’ in thre second transformed sentence?
In your example, you could say,
"It has been an hour since the bus left",
but you cannot say,
"It has been an hour since the bus had left".
However, you could say something like this:
It has been an hour since the bus had left before it could be inspected.
In this case, you would be talking about an event in the past that had occurred before another event in the past occurred, which can effect the use of the past perfect.
If you said,
"It had been an hour since the bus had left",
then that would be fine, but the meaning would be slightly different from what you have stated in your original example. Here's a good link regarding the use of "since": http://www.bbc.co.uk/worldservice/learningenglish/grammar/learnit/learnitv174.shtml.