What intake did you use? If you used the 2001 Automatic intake, that could be the problem. 5 speed uses a different idle air controller than the 4EAT does.
wondering if thats your issue. both IACS will bolt up, but there is differences between the two at least in the Gen 1 EJ18 and EJ22
Yes I'm using the intake from the 2001 Auto. I've checked the part number on my IACV vs one on my friends 99 OBS 5-speed and they're the same. I'm wondering if the pin outs might be different though.