Steve B,
Yes, the IH Service Manuals have very specific instructions about removing the steel coiled roll pin attaching the trunnion shaft to the squash plate. They are good instructions to follow. However, the instructions only discuss a single pin. Apparently, there was a design change made at some point late during the 1X8/9 series and a second pin was utilized and the hole in the squash plate was drilled on through the back side. This change was to probably increase shear strength/torsion capability of the joint.
When you drive top pin down to the recommended dimension depth to get it fully in the trunnion shaft, it also drives the lower pin into the squash plate. Following the Service Manual instructions is recommended but sometimes the lower pin can still catch the edge of the hole and preventing removal of the trunnion shaft, BTDT, as I discovered this while working on my 169 rebuild while trying replace the trunnion seals.
I ended up driving the top pin on through the trunnion shaft which drove the lower pin out of the squash plate. That's when I discovered there were two pins rather than one. As long you rotate the trunnion and squash plate so the pins aren't perpendicular to the back of the hydro housing, there is adequate clearence and there is no problem removing the pins in this manner.