Is my timing 180 degrees out?

[180sxdan]

I'm wondering if the CAS on my SR20DET is out by 180 degrees as when I check with a timing light I can only see all the marks on the crank pulley with the spark from cylinder 3.
When I use the spark from cylinders 1 and 2 I can't see any marks on the pulley from the top, but I can see them both from under the car about 180 degrees/pretty much opposite where they should be.
I haven't checked cylinder 4 because I can't fit the inductive pickup on coil 4 but I would assume I would be able to see the marks from that from the top like cylinder 3.

I'd just like to make sure this is the problem because if it was then I think my ECU would need to be running wasted spark ignition to keep running fine but in the settings it looks like it's not (Haltech E6X). My car has been running like this for quite some time btw.
If it is the problem I'd like to know if rotating the crank 180 or 360 with the CAS disconnected would fix the problem but I doubt it's that simple, this is confusing me because when I changed my camshafts I aligned the CAS as shown online using the yellow mark and the car does run fine like this.

Any input would be great.

Cheers.

[180sxdan]

I was able to get a signal from cylinder 4 today and it lines up with the timing light signal.
I find it weird that 3/4 show the timing marks but 1/2 are 180 out.
I would think that 1/4 would be together and 2/3 would be together as they are matched pairs, the pistons are in the same position albeit in a different stroke.

[JustinRB25s13'92]

what are you EFI configuration are you controlling timing with or are you just checking base mechanical timing?