"Not so much as...but..." or "not so much as...but as...?"

The first structure is correct.

I knew she would be standing here, waiting for me. No, not so much as waiting but expecting me to be here.

No need for as in the second part. The first instance of as used is a part of the idiomatic expression not so much as itself and not a prefactory to waiting.

The more common idiom however, is to place the as in the second part without but to convey exactly the same meaning.

not so much sth as sth

I knew she would be standing here, waiting for me. No, not so much as waiting but as expecting me to be here.

Neither rendition in the example is the best. Proper English idioms suggest the use of "not so much ... as ..." Example:

I knew she would be standing here, waiting for me. No, not so much waiting, as expecting me to be here.