One quick thought: when I mentioned having Wagon Trains as the settlers, it didn't occur to me that you could essentially replace the regular Citizen with Wagon Trains, thus having a settler that way. Then Wagon Trains could be painted black (or something) and be called Stage Coaches. Thus you don't have to do too much reworking (right?).
Ok, here's a tentative list of just the Founding Fathers.
Updated (with benefits)
Founding Fathers (Wild West)
Exploration:
Meriwether Lewis - 50% less travel time to Home City
William Clark - Strengthens relations with natives
John Slidell (negotiated the southern border of Texas w/ the Mexicans) - -50% cost of native land purchasing
Nat Love (famous African-American cowboy and frontiersman) - Free promotion (Exploration 1, Exploration 2)
Zebulon Montgomery Pike (American surveyor; mapped much of S. Louisiana Purchase) - Provides one Wagon Train
Jedediah Smith (hunter/trapper/trader; explored the Rockies and American Southwest) - +1 movement for Wagon Train, Pioneer
Bartleson-Bidwell Party (also better fit here, as they essentially started the Oregon Trail) - Provides one Homesteader, Wagon Train
Sacagewea (explorer who aided Lewis & Clark on their expedition) - +1 movement for Scout
Christopher "Kit" Carson (frontiersman and guide) - 50% faster production of Fort, Fotress
Benjamin Singleton (frontiersman; brought African-Americans to the west) - Provides 3 Homesteaders
Religion:
Gijsbert Haan (Dutch-born missionary who traveled extensively in the SW) - Provides 1 Expert Missionary
Joseph Smith (founder of the LDS church) - +50% conversion rate from missions
Pierre-Jean de Smet - (as is)
James Augustine Healy (first African-American Catholic bishop) - Strengthens relations with natives
Mary Baker Eddy (founder of the Christian Science movement) - +50% education; +25% conversion rate from missions
Hyrum Smith (advisor and avid follower of Joseph Smith) - 50% faster production of Church, Cathedral
Francis Asbury (famous "circuit rider" pastor in the Methodist Church) - Strengthens relations with natives; +3 crosses for every Town Hall
Walt Whitman (writer and forerunner of Existentialism) - 50% faster production of College, University
Billy Sunday (famous evangelical priest, Prohibition supporter, and tent revival proponent) - +2 bells per Church; +3 bells per Cathedral
Joseph Brackett, Jr. (famous Shaker songwriter) - +3 crosses per Church and Cathedral
Nathaniel Hawthorne - (as is)
Trade:
Jim Bridger (trapper/frontiersman, guide and advisor to Brigham Young) - as is in game
Joseph Glidden (inventor of the barbed-wire fence) - +25% cattle production in all settlements
Leland Stanford (railroad tycoon, founder of Stanford University) - Free School in every settlement
William Mulholland (engineer in California) - -50% tools required for buildings
Cornelius Vanderbilt (railroad and steamboat tycoon) - 50% faster production of Textile Mill, Tanning Mill, Packing Plant, and Whiskey Factory (some thoughts for name changes for buildings, maybe?)
Levi Strauss (American inventor) - +3 hammers per Town Hall
John Jacob Astor - (as is)
James Marshall - as is in MOD
Edwin Drake (credited with the first successful oil rig in America) - +1 food on plots with 2 food; +25% sugar, cotton per settlement
Military:
Andrew Jackson (U.S. President; fought against Native Americans) - Free Stockade in every settlement
"Liver-Eating" Johnson - as is in MOD
Maribeau Lamar (Gov. of Texas; strongly anti-Native American) - Free Promotion (Grenadier)
Davy Crockett (frontiersman; fought for Texas v Mexicans) - Free promotion (Formation); +1 movement for converts
William Travis ((in)famous proponent of the Texas "War Party") - Free promotion (Looter)
William C. Quantrill (Confederate guerilla leader) - +50% strength for converted natives
Daniel Boone (frontiersman, explorer, fought for Texas v Mexicans) - Free promotion (Ranger 1, Mountaineer 1)
George Custer (American general) - +50% vs Natives
James Bowie (land speculator; inventor of the Bowie knife) - Provides 2 Veterans
Wyatt Earp (American lawman) - Increases gun production by the tax rate
John Coffee Hays - as is in MOD
Politics:
Thomas Jefferson (U.S. President at the cusp of the "Wild West" era) - +1 cross per town hall
Jim Beckwourth (famous African-American pioneer) - Strengthens relations with the natives
Samuel Clemens (writer) - as is in MOD
Kenneth Lewis Anderson (Speaker of the House in Republic of Texas Congress) - +3 bells per town hall
Francis Scott Key (composer of The Star-Spangled Banner) - Increases liberty bells production by the tax rate
James Henry Lane (fundamental in the organization of the Kansas-Nebraska Act) - Provides 1 Homesteader; -25% native land purchasing
Robert Livingston (American Ambassador to France; Negotiator of the Louisianna Purchase) - Increases hammer production by tax rate
William Jennings Bryan (gave famous "Cross of Gold" speech) - +3 crosses per University
Laura Ingalls Wilder (writer, early feminist, frontierswoman) - +1 bell per schoolhouse; +2 bells per college; +3 bells per university
Kintzing Prichette (lawyer and governor of Oregon Territory) - +3 guns per armory, magazine, arsenal
Harriet Tubman (famous Underground Railroad proponent) - Strengthens relations with Natives; Provides 3 Indentured Servants
Also, I was looking at the leaders, and I thought I might suggest some different ones (I know this would change your leader heads and stuff, but I thought these might be more authentic - thus making the MOD more awesome). I've included "kings" for territory, too, and an additional two territories.
Leaders: Wild West
Oregon Territory - James Buchanan, U.S. President at the time
Joseph Lane - initial governor of Oregon
George Law Curry - helped create Oregon as a state
Utah Territory (State of Deseret) - Zachary Taylor, U.S. President at the time
Brigham Young - founded Utah/Deseret
Caleb Walton West - governor of Utah Territory; help give Utah statehood
New Mexico Territory - Millard Fillmore, U.S. President at the time
James S. Calhoun - first governor of New Mexico Territory
William Mills - governor of NM Territory and justice on NM Territory supreme court
California Republic - Antonio Lopes de Santa Anna, essentially lost California
William Ide
John C Fremont
Republic of Texas - Sam Houston, president of Texas for two terms
Stephen Austin
David G. Burnet - interim president and first Sec. of State for Texas after annexation
(This one I'm totally cool with nixing; it was just around in the "Wild West" period)
Minnesota Territory (?) - James Polk, U.S. President at the time
Alexander Ramsey - first governor of Minnesota territory