Hello. I arrive in Madrid on April 15th 9:05 am. Plan was to train to Pamplona then bus to SJPP. Why are all the bus routes on the Rome2Rio site 5 hours long. I keep hearing there buses that are around 2 hours. Where do I find these? Also I've never flown into Madrid. Does it take long to get through customs? Should I give myself a couple hours relative to booking a trane?
If you take a train after you arrive in Madrid, you won't get to Pamplona in time for the bus to SJPDP which leaves around noon.
You can either stay a night in Madrid and take the early train to Pamplona to catch the bus or train to Pamplona and spend the night and catch the bus the next day or even begin walking the Camino from Pamplona as many others do.
You can also take a cab from Pamplona to SJPDP when you arrive and there will likely be other pilgrims on your train who you might share the ride with.
Public transportation in Spain is very good, but it isn't always exactly the schedule we can keep with a personal vehicle. It is a Camino and you'll soon experience life at the pace of walking so these delays will help you ease into that slow down.