None of the iberian Kingdoms are big.Just keep Portugal make sure you have ALL the dejure counties of the Duchies.(in Iberia)So the Duchies will Drift into Portugal.It is just a matter of choice as to how many vassals you want to deal with.
The faction system onlyREALLY works in a single Kingdom that is mostly De Jure otherwise the mechanics screw up.I played an HRE game(Count to HRE Emperor) and had many of the problems you are describing.(HRE had invaded Iberia and N Africa before i became Emperor) Basically you have to think when expanding to what is next door as opposed to what is within reach and weak.
The faction system onlyREALLY works in a single Kingdom that is mostly De Jure otherwise the mechanics screw up.I played an HRE game(Count to HRE Emperor) and had many of the problems you are describing.(HRE had invaded Iberia and N Africa before i became Emperor) Basically you have to think when expanding to what is next door as opposed to what is within reach and weak.