Hi Dave,
In Civil Engineering, often there are major discrepancies about the surrounding items that are just to give an idea as to what is around. The client is paying to get a specific item done (his property) and does not want to pay for exacting locations of the items not on his property (assuming he has permission to access other's property).
The general alignment of the A&NM looks right compared to the photo. Once the field notes were reduced and drafting started on the MS, the civil engineers probably would tell the draftsman that somewhere here there was a river with a pointing finger. The draftsman (not having seen the site) would make a very rough representation of the location - nothing accurate since no field notes were made of the object in question (either the A&NM or the rivers).
As for the wye not feeling quite right. It might be something as simple as land movement over the years since the MS was abandoned. Remember Cerro Summit experienced constant slippage below a mesa that was possibly due to irrigation on top of the mesa. The track was relayed each year for the stock rush and then removed for a while (as I recall).
Also recall Kyle's Kink on the C&TS. Assuming the rails were pulled and then the area allowed to weather, in 40-50 years armed with the "original plans", the ROW would look wrong. Same goes for the valuation plans and the too long tail track at Big Horn wye.
Just food for thought.
Doug vV