Can I get a 144-Hour Visa-Free Transit twice for this itinerary?

Yes that is considered two separate 144 hour transits for Spain passport

I am not sure this is correct. My itinerary is miami -beijing (5days) - kiala lumpur 6 days - shangai 3days and back to miami. I read this might not be done with 2 144 hrs visa free but rather get a china visa at the consulate before departure. I emailed the consulate but they have no responded

You are able to apply for 2 144h twovs in Beijing and Shanghai in both trips. No visa will be needed then. Nice trip.

That's perfectly fine for 144-hour TWOVs in Shanghai and Beijing unless you have a hidden stop in China or elsewhere that you've overlooked.