Here are the individual leaders from my test using the above mentioned settings. My stolen bases are too high because I forgot to change all teams tendancies before this run.
Overall not bad results for no player editing aside from Nap Lajoie's homers as mentioned above.
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AMERICAN LEAGUE Individual Leaders
BATTING
REAL LIFE 1901 TEST SIM
.426 Lajoie .432 Lajoie
.340 Donlin .367 Collins
.339 Freeman .344 Keister
HOME RUNS
14 Lajoie 11 Grady
12 Freeman 11 Davis
9 Grady 10 Freeman
Doubles
48 Lajoie 44 Anderson
46 Anderson 42 Cross
42 Collins 41 Collins
Triples
21 Keister 26 Keister
21 Williams 23 McGraw
17 Mertes 20 Duffy
SB
52 Isbell 57 Barrett
46 Mertes 51 Hoy
38 Jones 49 Jones
PITCHING
ERA
1.62 Young 2.40 Griffith
2.42 Callahan 2.48 Callahan
2.61 Yeager 2.78 Young
Wins
33 Young 31 Young
26 McGinnity 27 Wiltse
24 Griffith 25 McGinnity
Strikeouts
158 Young 145 Young
127 patterson 137 Garvin
124 Dowling 132 Patten
NATIONAL LEAGUE
BATTING
REAL LIFE 1901 TEST SIM
.376 Burkett .382 Delahanty
.354 Delahanty .375 Flick
.354 Sheckard .353 Kelly
HOME RUNS
16 Crawford 13 Crawford
11 Sheckard 13 Delahanty
10 Burkett 10 Davis
DOUBLES
38 Daly 51 Jennings
38 Delahanty 45 Delahanty
37 Wagner 38 Donovan
TRIPLES
19 Sheckard 21 McCreery
17 Flick 21 Hartsell
16 4 players 21 Davis
STOLEN BASES
49 Wagner 56 Vanhaltren
41 Hartsel 54 Davis
40 Strang 53 Demontreville
ERA
2.18 Tannehill 2.00 Phillippe
2.22 Phillippe 2.21 Poole
2.27 Orth 2.36 Orth
WINS
25 Donovan 31 Phillippe
23 Harper 26 Harper
22 Hahn/Phillippe 26 Powell
STRIKEOUTS
239 Hahn 227 Hahn
226 Donovan 166 Waddell
225 Hughes 143 Nichols