Need help! Mustang runs like crap

I have a 08 mustang gt that i bought last year, love the car but recently my throw out bearing let go. i dropped the transmission replaced throw out bearing and upgraded to a stage 2 clutch. before the original throw out bearing let go i had a problem where if i pushed in my clutch pedal my rpms would go from 1k and drop down to aboout 300rps or just die out. so after i did the new throwout bearing and stage 2 clutch i went to start the car and noticed that i still had the rpm dropping problem when the clutch is pushed in. so i decided to run the dtcs and came up with p0345 code. took a further look into and realized that the connector for the cps was rotted so i replaced it and now i have codes for both of the cam sensors and whenever i start the car at idle it will shake all over the place like its misfiring. would love to get anyones input on it before i bite the bullet and send it to a shop.
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