I put older heads (2003) on my 2006 FLHR do I need to change my intake manifold

 

No you don't. However, the 03 heads have more exhaust port restriction than the heads that came stock on your bike.

 

parts book part #s for manifold and flanges not the same

 

Correct.

You will need to use early TC88 manifold flanges. I may have mis-understood your question. I thought the question was "can I use my INTAKE?". The answer is yes you can. You will need to use different flanges.

 

Why the change to the '03 heads?

 

Hmm...didn't want to ask this question below here?
why-did-hd-change-manifold-and-flanges