I know that the AFM plugs are different. I've just done a Neo swap into an R33 series 1.5 and found that most stuff plugged in. I'd assume that there wouldn't be too much difference.
Here's a thought - as long as you've got the s1 parts and they work, just bolt them onto the s2 motor. Therefore you don't have to change much. I ended up retaining my r33 AFM and throttle body because I didn't want to change all my wiring to use the r34 parts.