A vac leak could cause that, but so could having left a number of connectors off.
When I did my intake (in the last few weeks), I'd forgotten a few connectors...and had the EML light...and CEL. As I started plugging things in, the lights disappeared!
That round connection to the icv gives a number of people problems...but you can reach it by just removing air box. I don't think you can wiggle around the intake too much, but maybe if that stud is in the right spot, you could get to it.
Don't forget that bolt on the bottom of mani prevents it from sliding down at all...and as it's plastic, you don't want to be bending it around too much.
Sucks. BTW, I didn't remove fuel rail at all...just the plugs for injectors...by pulling off the little wire clips on them. Don't lose them!
Also, you don't have a lot of free play from those vac lines or the fuel supply hoses in back either I don't think.
Definitely sucks! None of the stud is sitting proud of the intake mani?