The 90 day rule does apply for vacation stays only anyway. If you want to work in the EU, if you still have no residency, you need a work visa, which has to be applied for in every country of the EU separately. The rules for those vary wildly and the process can be very long, complicated, costly and frankly impossible as the employer might have to prove he cannot find EU citizens able to do the job.
Anyone who has a job in the EU before 31st of december and moved there before that day, should be able to apply for residency and stay in the EU, however, that might have some rules as well including maximum amount of days out of that country or one could lose residency rights.