Meeting the requirements of the law are not an undue burden, and administrative requirements like the 90 day report are pretty flexible in before and after the reporting date...even then, the fine can be paid without muss and fuss.
Most foreigners need not fear, only those that are actively trying to break or skirt the law in a grievous manner should. There are no jackboot thugs breaking down doors in general sweeps of everyone they come upon.
Just remember, while they are working on your documents prior to your appearance for the stamp in your passport, you are ‘in process’, and any defects they perceive, unless egregious lies, you will be allowed to be corrected with information or documents they require.
Follow the instructions given to you by your immigration office about what documents to have. Make sure you have two sets of all of them...especially the house register. When you go to immigration to apply have the original documents with you if there are any questions.