Portugal: white (primary), blue (secondary)
These were the colours of colonial portugal, the green/orange came in post colonial era.
England: Orange red (primary), yellow (secondary)
Leave red for Canada, Australia or South Africa.
Aztec/Mexico: Dark Green (former portoguese, primary), white (secondary)
Aztec or Mexico never used the light green.
Japan: Light cream (primary), red (secondary)
light cream coresponds to crysanthemum, traditional japanese symbol.
Germany (HRE): Black (primary), yellow (secondary)
Black isn't used, yellow is used widely, so using black as primary colour for Germans can leave room for one more colour.
Mayan/Colombia: Yellow (primary), blue (secondary)
The colours of Colombia are yellow, blue and red. Yellow occupies around 50% of the flag, so it should be the primary colour.