Translation:Don't harvest the pebots yet! They are not ripe!
I almost translated this first sentence as "Harvest three pebots." Is there any mechanism that could be used other than context to differentiate between wej the number and wej the adverb?
Not in this sentence; it's entirely determined by context. The course will usually accept both possibilities as translations.
In other sentences you may be able to tell them apart by word order. In wej yIQong Don't sleep yet! the wej has to be the adverbial not yet, because Qong doesn't take an object. (You can't say Sleep three!)