2003 Other Lincoln Models P1336 Code, engine shakes at idle

Hi this is jonathan. I have a 2003 Lincoln Aviator, and it has been running rought at idle (it shakes alot) and at acceleration. When backing up you can feel hesitating going back, then once you put it in drive it keeps doing the same thing. It does this every 3 minutes or so. Also there is a long beep noise (2 seconds) coming from with in the dash somewhere. This only happens every now and then and it started when the truck started acting up. 3 days went by and a code poped up, P1336. I replaced both the crank and the cam sensor, (the cam sensor is a ford part but the crank is from autozone) but the truck keeps doing the same thing. The code has not come on yet but I've only driven it for 12 miles. Could the code be related to the truck acting up? An employee from autoze told me that the PCM might be going bad. Could this be also true? I know it is kind of hard to diagnose a problem if you dont have the truck to look at but any information would be greatly appreciated. Thanks.