Custom POS tags with SpaCy for NER
For your first question, I would try to use Regex to identify the reference numbers since they seem unique comparing to normal words. I assume they are:


All capital
Start with one or more letters
After follow numbers
Any other pattern may follow (i.e. letters, numbers, hyphens)
Do not include spaces 


Could be something like this: \b[A-Z]+\d+([A-Z]|\d|-)*\b

I can imagine you could do it better...