Evidence: The two aerial shots below show show where current and past known lines were, plus my doodling of speculated lines. This imagery is from 1993 imagery on Google Earth. 1954 imagery from Historical Aerials (copyrighted) is even more clear. Follow the link, enter N44 31.600 W85 23.950 into the search box, then select 1954 imagery.
On the imagery below, The dark red shows the current configuration. The dark purple is where the Manistee & Northeastern River Branch passed through and under the GR&I from 1909 through 1925. The bright red shows what I believe to be past GR&I grades that appear to define a previous wye configuration, plus a siding. The pink line is a current trail at a somewhat lower elevation that may also have been a siding. I have seen (from the pink trail) the grade of what I used to think might have been an interchange between the GR&I and the M&NE ( marked with an X on the annotated image), but could never make a connection to the M&NE. The property east of the pink trail along the purple M&NE main is posted so I didn't venture there. After looking at the 1954 imagery, I now believe this was the old south leg of a previous wye, plus a siding within that wye. As I stated up front, my imagination tells me that when the M&NE built the River Branch, the GR&I wye was reconfigured to avoid having multiple bridges over the M&NE.
Also on the imagery is a light purple line that I believe to be an interchange between the M&NE and the GR&I. Information that I have seen from multiple sources does not indicate there was an interchange between the two, but the M&NE did make use of the GR&I depot for its passenger trains. I have seen a photo of M&NE flats being loaded with gravel on a siding at Walton with the water tower in the background.
1993 imagery from Google Earth
1993 imagery from Google Earth with my doodling
Does anyone have information that would back this up or blow that theory out of the water? Please feel free to mark up my imagery and repost if you have a different idea. I have my own doodling of what I believe to be the layout of the station area of Walton if anyone would like to see it, but I wanted to bounce this moving wye idea around first.