I have a 2003 fatboy and and 96 fatboy, can these intechange without too much trouble?

 

3/4" and 1" axles.
But they sell replacements.

 

Define "without too much trouble".
It is not a direct replacement.
You can adapt, measure and acquire correct spacers and then review alignment of rotor with caliper.
A review of rear pulley would need to be made since it most likely will require a spacer too.
Then if doing the front wheel..similar but you need to review speedometer drive if current speedometer is not digital.
I believe 2003 had a wheel that was 0.5 inches wider so clearance would need to be reviewed.
Doable but you would need to define "without too much trouble".