ways to code for better speed of processing date comparisions / slicing in python
There are a few small niceties that you can add.
long = pd.DataFrame(columns={'bene_id', 'day','date'})
cols_to_order = ['bene_id', 'day','date']

should reuse the list:
cols_to_order = ['bene_id', 'day','date']
long = pd.DataFrame(columns=set(cols_to_order))

This:
cols_to_order + (long.columns.drop(cols_to_order).tolist())

can drop the outer parens, since . takes precedence over +.
e, j and temp need better names.
This:
for i,j in zip(range(1,91), Series(date_range(start,stop))):
    long = long.append(pd.Series([e,i,j],index=cols_to_order), ignore_index=True)

shouldn't be a loop. There's almost certainly a way for Pandas to vectorize it.