Are word order and word relationships aspects of semantics, morphology, syntax, or orthography?
Word order is a part of syntax because it decides how to build different kinds of sentences.
For example if we look at the sentence I am writing a letter. Its word order is S - V - O (subject - verb - object), which makes the sentence indicative.
If we change the order to V-S-O (i.e. exchange verb with subject): Am I writing a letter? the sentence becomes interrogative (question).
On the other hand word relationship is a part of morphology. It studies how can we create one word from the other by adding parts (called morphems).
We can list many morphems (parts) which turn the word, to which they are added, to its opposite. Examples of such morphems can be:
im : patient
And so on.