Good questions as always,
1: These ganglions may arise from any of the sources you have suggested. They can be from FCR sheath. They can be from the radio-carpal solar ligament complex (these are most common in my experience). They can arise from the proximal row intrinsic ligament complex. It may be impossible to be absolutely sure on ultrasound and MRI may help to clarify if it is important.
2: Yes I always see a slight flattening as the median nerve goes under the transverse carpal ligament (TCL) at the level of the distal lunate / capitate. I think it is normal for the nerve to look slightly wavy approaching the TCL and then look a little more “ironed” when it goes under it.
This does not indicate a step sign in my view. For a positive finding I need fascicle oedema proximal to the TCL with an abnormal cross sectional area and abnormal WFR. Then you see real compression and an obvious step sign. The presence of a normal cross sectional area and WFR indicate a normal examination for me.
3: I lock the PIP and flex the DIP only as this moves just the PFD tendon. Then I flex the MCP and DIP together to watch them both slide.
Sometimes it is the FDP that gets stuck and I will share a case of this with you soon. Mostly it is common for the FDS to get stuck or both together.
4: I look at the scaphoid and trapezium as I don’t get such a good look at the trapezoid. Looking at the scaphoid and trapezium is fine for seeing the arthritis.
I can’t see the image you posted. You may need to re-upload it.
5: I put the cross sectional area and the WFR on my worksheet as well as the myriad of other observations I make in general assessment of the nerve, the tunnel , the articulations and the thenar muscle bellies.
Steve