This construction reminds me the way Yoda speaks.
How is it known that the sentence doesn't mean "We wake the late comrades"
For that sentence we would have to use the adjective serus, sera, serum with comites.
comites seros excitamus
Does it matter what order you put the words in, if the cases are correct?
Word order can matter in some sentences. It doesn't matter in this one.
Does comites translate as comrades meaning friends or mates or as comrades meaning fellow soldiers?