I'd bet money that you didn't install the CPS correctly. Don't feel bad, I did it too the first time I removed it like 2 years ago.
That brown connector that looks like an injector connector is for one of the VSV's that mount underneath the intake manifold.
That 12" hard vacuum pipe near the air box, the nipple near the motor goes to the BVSV on the top of the thermostat housing, its blue. The nipple that is farthest from the motor goes to the charcoal canister. Both vacuum lines that attach to this prebent hard pipe are about 16" long, maybe shorter.
Now that you already turned the motor over and installed the upper timing belt cover, finding the correct TDC is going to be slightly hard unless you drop the coolant and take the thermostat housing off to take the upper timing belt cover off to line the notches up with the cam marks. I hope you can understand what I just said. Only other way to find the correct TDC without dropping the coolant and taking the thermostat housing off, is to take the No.1 cylinders spark plug out and turn the crank with a rachet and when the crank nears the 0 mark on the lower timing belt cover listen to how much air comes out of the spark plug hole, if you hear a rush of air come out you are on TDC of the compressions stroke (all valves closed) if you dont hear any air come out you are on TDC of the exhaust stroke (exhaust valves open, air is escaping out of the valves instead of the spark plug hole). I suggest just dropping the coolant and lining the cams up.
Now, when you find the correct TDC, you have to install the CPS a certain way. I think its page IG-22 in the TSRM. Pretty much, when the CPS is installed correctly the rotor is about 1/2" to the right of the top pickup coil. I can post a picture if you need it. The TSRM explains how to line the drilled mark on the CPS shaft with the groove on the CPS housing which will line the rotor tip exactly with the top pickup coil. It's really not that hard, let me know if you need a more through explanation with pics.
Good luck.
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