OK, I got it figured out! I was on the right track but what I failed to realize was that my 1946 was on a fresh install and I hadn't set up my controller for it yet. After I set up my controller in 1946 I went into its config file and sure enough the proper values were now in there. I simply copied and pasted from the 1946 config to the CoD one. Here is what it looks like:

[rts_joystick]
X=0 1 4 9 16 25 36 49 64 81 100 0
Y=0 1 4 9 16 25 36 49 64 81 100 0
Z=0 10 20 30 40 50 60 70 80 90 100
RZ=0 10 20 30 40 50 60 70 80 90 100 0
FF=0
U=0 10 20 30 40 50 60 70 80 90 100 0
V=0 10 20 30 40 50 60 70 80 90 100 0
1X=0 1 6 10 15 22 33 44 58 72 100 0
1Y=0 1 6 10 16 23 31 43 56 73 100 0
1Z=0 100 100 100 100 100 100 100 100 100 100 0
1RX=0 100 100 100 100 100 100 100 100 100 100 0
1RY=0 100 100 100 100 100 100 100 100 100 100 0
1RZ=0 1 4 8 13 21 28 39 52 69 100 0
1U=0 100 100 100 100 100 100 100 100 100 100 0
1V=0 100 100 100 100 100 100 100 100 100 100 0

This, everyone, I have confirmed to work! You need the 1X values for it to work not the X values, the axes with the 1 infront are what windows uses to set the joystick sensitivity.

Perhaps this should be stickied so everyone can benefiet from this.