I think your confusion is coming from lack of exprecience with EU regualtions.
1. JAR OPS is no longer valid and replaced by EU OPS which is issued as EC Regulation and available free of charge in all european languages on EurLex and many other websites along with other related regulations.
2. Basic rules on operator certification are contained in EU OPS, however EASA is not certifying carriers, it is down to national aviation authorities who may have some additional requirements and procedures. You need to contact your national european authority to get more info.
3. There is no such thing as Part-121 or Part-135 in EU. There is a singe regulation covering everyone commercial starting from single Cessna Mustang operator up to Lufthansa and KLM/AirFrance.
4. Don't worry about NPA, this is not something of a daily concern for EU operators.
5. I somehow guess you looking to setup an airline in Euroland without having first hand knowledge of regulations here. If I'm about to do that in the States with very sketchy knowledge of FAA regualtions, I would employ someone who knows. Recommend you to do the same.