Allow me to have a go at these points:
The line that PZ1 crossed is most likely the former Milwaukee Road line from Wabasha, MN through Eau Claire, WI, to Chippewa Falls, WI which indeed followed the Chippewa River. In addition, at the town of Red Cedar, WI, (about half way to Eau Claire) there was a branch line which went north to Menomonee (Junction), WI. - at Menomonee the lined T’d into the “Omaha” line (on the route of the Twin Cities 400), and the northern end of that line remains as a wye. Of course, Wabasha, MN, was located on the Milwaukee Road main line between Chicago and St. Paul. At Chippewa Fall the Milwaukee Road line T’d into the SOO Line.
Where Highway 35 crosses the former Green Bay and & Western tracks both are running more or less east and west, and thus NOT at right angle to the highway, and this is several miles from the BNSF line. The point where the GB&W (Wisconsin Central) line T’s into the BNSF is almost inaccessible by road vehicles. At one time there was a bridge west of that point that crossed the Mississippi into South Winona, but its 100 year life ended in 1989 (not to be confused with the former C&NW bridge which crossed the Mississippi right next to the current highway bridge).
The BNSF line never intersected with the C&NW line to Galesville. That line ran from Trempealeau Galesville (7 miles). The BNSF line runs along the Mississippi River on the west side of Trempealeau, while the C&NW “main” line, and the turn out to Galesville, was on the east side of town. The C&NW “main line” is a bike trail (101 miles from Reedsburg, WI, via Elroy, Sparta, Onalaska, to the Wildlife Refuge about five miles north of Trempealeau). North from there the C&NW went through some wetlands, and crossed the GB&W line at Marshland, WI. Most of the C&NW line from Marshland to Winona was covered over by the widening of the right of way of Highway 35/54. An effort is underway to construct a bike trail extension from the Refuge to Winona. The only place in Wisconsin where the BNSF and C&NW main lines crossed was there east of Winona just before the C&NW crossed the Mississippi (although the C&NW branch line into La Crosse crossed the Q line at “Grand Crossing”). And yes pieces of that C&NW bridge over the Mississippi at Winona remain (but not the swing portion). The C&NW Trempealeau-Galesville line was abandoned years ago, (late 40’s), and today is almost unnoticeable, save for some tree lines.
The La Crosse and Southeastern, (which ran from La Crosse, through Stoddard, Chaseburg, Coon Valley, and Westby, before arriving in Viroqua, WI.) was shut down in 1933 (although the line from Chaseburg to Westby was purchased by the Milwaukee Road and used through 1972 - the Milw. Rd. had its own line from Sparta to Viroqua, via Westby. In its day, the L&S used the Burlington (downtown) depot and ran on CB&Q track to the south end of La Crosse, and then had its own line from there to Stoddard, running next to (east side) the Q line. 99% of the entire L&S line is lost to erosion, but we did find some old spikes using a metal detector.