2. Are there defunct lines nearby or that were predecessors to the Milwaukee?
Predecessors (in whole or as parts) I'll leave the research as to whether they were "nearby" to someone else:
Bellingham Bay & British Columbia Railroad
Bellingham & Northern Railway
Bellevue & Cascade Railroad (narrow gauge)
Chicago, Milwaukee and St. Paul Railway
Chicago, Milwaukee & Gary Railway
Chicago, Terre Haute & Southeastern Railway
Chicago & Pacific Railroad
Chicago-Buena Park
Chicago North Shore & Milwaukee
Chicago Rapid Transit
Dakota Southern
Dubuque Southwestern
Illinois, Iowa & Minnesota
La Crosse & Milwaukee Rail Road
La Crosse & Southeastern
Marinette, Tomahawk & Western Railway
Milwaukee and Mississippi Railroad
Milwaukee and Waukesha Railroad
Montana Railroad
Milwaukee & St. Paul Railway
Milwaukee & Prairie du Chien Railway
Milwaukee & Northern Railroad
Puget Sound & Willapa Harbor Railway
Racine & Mississippi Railroad
Sioux City & Dakota
Sioux City & Pembina
Seattle, Port Angeles & Western Railway
Tacoma Eastern Railroad
Three Forks-Salesville and Menard
Western Union Railroad
White Sulphur Springs and Yellowstone Park Railway
3. What geographic features are nearby that would be plausible railroad names?
I'm partial to "bitterroot"