Make an appointment to speak with the head of that precinct, take in all the evidence you have on your stalker being your stalker, and show it to them. Ask if it is common for their officers to take the word of someone with a pattern of law breaking and obsessive behavior over that of their victim. In the future- though I would hope there isn't a third time- if someone breaks into your house, DO NOT ENTER IT. If you see signs that a break in has occurred, call the police, have them come out, and wait in the yard in your car, with the doors locked and windows rolled up. Wait until the police clear the house. Entering a house that has been broken into puts you at risk of the burglar still being there and being directly attacked by them.

Wait, you have to contact the person you are filling the restraining order against? In the US, at least in Florida, the person is "served". In cases like this, and in domestic violence cases, law enforcement will serve the papers for you. See if anything is available by calling local non-emergency.