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Limp mode in manual?

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2003 mazda 6s
I traded my car for a 2003 Mazda 6s and thought I was trading up. So far I have been proven wrong. There is an oil leak which I believe is what put the car into limp mode the first time. Would not Rev past around 2300-2500 rpm and was grunting like a warthog at idle. That was at the same time that the alternator went out. I put a new alternator in and added oil, which made the car run normal like it was. About 3 weeks later, it seemed to put itself back in limp mode. I added oil and it's still in limp mode. While taking the intake plenum off I noticed two connectors not plugged in and a vacuum lone not hooked up. I also don't have an emission line running on the top of my throttle body. My codes are p0300, random misfire. P0850, neutral switch input circuit problem. P0507, idle control system rpm higher than expected- my rpm is about 1200 unless the clutch is pushed in then it drops to about 800. P0325, knock sensor malfunction. P0480, condenser fan relay control circuit malfunction- I assume from the fan being jerry rigged to a toggle. P2198, o2 stuck rich bank 2 sensor 1. Reading from a few forum discussions, I have gathered that the knock sensor is under the plenum or under the rear exhaust manifold. I climbed under the car to see if I could see it and found that one of the connecter appears to go to the transaxle seeing how there is a plug with no connector. I'm not sure where to go from here, but plan on getting back out there tomorrow as it's 9 and snowing. I apologize for the very long post and appreciate any advice. Thanks in advance
 

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