Cyl 1-3 Timing Out on 3 chain engine after IMS replacement

[B6T]

After drilling out the two broken exhaust manifold bolts (grrr...), I was able to re-assemble the car and get it back on the road. I've driven approximately 200km so far. The CEL illuminated at about the 10km mark. I read the code out with a generic OBD2 reader and got a P0012 code, which is:
"P0012 - "A" Camshaft Position - Timing Over-Retarded (Bank 1)"

I'm assuming that this is the intake cam, but would appreciate if someone could confirm. I understand the exhaust cam doesn't have a position sensor so I'm not sure how the DME could pick this error up anyway.

As noted above, I didn't touch the cam timing on the intake cam because it would have required loosening the TTY bolt and I didn't have a replacement. Looking back, I think what might have happened is that the cams skipped two teeth, instead of only one as I had originally thought. This would explain why I had to set the cam timing on the exhaust cam, when I really shouldn't have had to considering I was putting the cam "back to where it was". Then again, if I indexed the cam two teeth, it wouldn't necessarily have been in alignment either. This was a few weeks ago now, so my recollection is a bit hazy (also a side effect of working 60 hour weeks...).

So I've been searching about how to set the intake cam timing on the three chain engine, including reviewing the factory camshaft allocation procedure, and there is a gap in my understanding.

I understand that three tools are required for this job, the TDC pin, the typical camshaft holder which does in the green-plug end of the head, and the stay bar that holds the body of the intake cam while tightening/loosening the TTY bolt that holds the cam adjuster into place.

The question I have is when you loosen the TTY bolt out of the intake cam, 1. can you remove it entirely without the cam coming off, and 2. can you then index the cam adjuster on the end of the camshaft while holding the cam in place with the cam holder tool?

The second question relates more to the geometry of what restrains the cam adjuster on the end of the camshaft, i.e. is it a simple clearance bore, is it a taper, or is it some sort of shape and the position is fixed?

Basically I'm trying to figure out the specific steps I'm going to follow to set the cam timing with respect to how I loosen each cam, when I set in the alignment tool, and when I set the TDC pin, given that I can't turn the engine backwards.

Thanks for all the help guys/gals.