I have swapped the mounts over and everything it just won’t seem to line up to the motor except for one side

 

Sorry can't help with that part
Generally speaking you have to re-drill motor mount holes in frame when changing engine sizes, or make a custom plate, which ever is easier

You do know that 2006 is a full digital Ranger unlike the 2003, so can't use 2003 computer, and 2006 2.3l computer can't run the 3.0l engine

 

I am just asking... Why a 2003, 3.0L V-6 ?

Although the 3.0L seem to handle some abuse, it is ssssoooo low on horse power, there are better choices and I am not talking a 5.0L but that too is a good choice.