1999 Volkswagen Jetta please

I was wantin to know if u could tell me what you think would not be letting our car start? We went to crank it up and it would start. We had someone test the battery and it was perfect. Our dealer just put a used motor in it and put a new altinator on it. The windows wont roll down the lights won't come on the horn won't beep and the trunk won't open with the button! Usually when we lock the doors on the outside it will chirp and the lights with blink none of that is happening now and i was wonderin if it was the security systems and how would be fix it? We only got one key and the key only fits the eginition and the door! It won't fit the trunk nor the dash!Please tell me how to fix this problem???