Why did putting an intake in my car screw the whole thing up?

i have a 2000 pontiac sunfire and i got rid of the entire stock intake and put in a tube from the throttle to a cone filter. i put the sensor in and put the hose on to the spout on the valve cover, like how it was with the stock intake, and im pretty sure everything is completely sealed. now it shifts hard, jumps, traction control is off, and something squeaks when it shifts. i need to fix it by tomorrow and preferably without putting the stock intake back in. its an automatic.