1. I'd probably pull the motor just because this is your first time, and its much easier out of the car, not to mention it will be easier to fix all of these " missing or cut " connectors you have.
2. My question to you 1. Why did you buy the car with a bunch of cut/missing connectors? 2. What makes you think that it is " set up for turbo or swapped " ?
Just aggravates me that people post " Just got DSM already a problem " when the problem has nothing to do with the car. Some tool cut and jerry-rigged it, and you bought it, and some how it having problems is the norm because its a DSM? Blah.
Good luck making it right!