How to I get a TM with lowest index?
If I understand your question correctly, then it simply asks for the TM with the encoding who is ordered first in the lexicographic ordering.

As you surely know, many TMs perform the same task.
Look at all the TMs that accept anything but empty set. Look at the encodings of all of those. Each encoding is simply a string. If you write all those string ordered using the lexicographical ordering (like in the dictionary), which string comes first? That should be your answer.