my buddy has an 06 which has a 88 i have 07 which hasa the 96..... like people said before there is 3 things possible. 1- motor blown replaced with an 07 motor, 2- bike build in 06 but is an 07, or 3- has a bore kit in it.

 

06 was an 88 with a 6 speed.
only year you'll ever see that combo.
They always try out new parts on the dyna 1st.
The 10th digit of the vin tells what year.

 

Definately not an 06 with a 96ci.

I bumped mine up to a 95ci but it still would be registered as an 88ci. Sounds a little fishy to me.