Actually, I think I figured out the issue. The Bellorphon variant, was purchased on holodeck. Then we were allowed to transfer more characters to tribble. I transferred my officer with the new ship variant. Note I did not purchase the new variant on tribble. So when I was in the customize window and trying to change parts it would not let me because I had not bought the variant on the tribble side. Oddly at no time during the process did it tell me I needed to purchase the new variant. Normally the purchase section would of had the C-points required, but it was not displaying. It took me a little bit of time to figure it out. But I went to the ship store on ESD and got the Bellorphon variant. Once I had it, I could then customize the ship to use the intrepid pylons and nacelles. So it was not a bug as I thought. Thanks for the feedback guys.