I would go back through everything you've disconnected and make sure everything's plugged back in first. I missed plugging the throttle body position sensor back together this weekend after doing some extensive maintenance, but from the codes I figured it out fairly quickly. If it was running fine before, and it's doing what you're describing, that sounds like either something didn't plugged back in, or a wire was damaged--hopefully not the latter, that's a major pain. It's going to be tough to figure out without codes; it could literally be anything from an unplugged sensor to a torn intercooler boot. But I'd start by going back through every sensor you unplugged along the way and double check that they're all reconnected properly. It's the easiest place to start.
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