Ok... normally when I shoot, I either shoot an AR or I'll shoot my handgun in a range session. Can't recall ever shooting both in one outing. Anyway I was out shooting last week and decided to practice some CQB stuff while shooting the AR at about 50yards.
Shot about 20 rnds in the AR,
pretends the rifle jams,
drops it and grabs the handgun from the holster,
immediately when I draw on some 20yard targets, I notice I am taking to long to get on target with the handgun.
The problem is that I have always been taught to look "through" the sight "Eotech" and focus on the target with the AR and have always focused on the front sight and not the target with the handgun. It's this transition from AR to handgun and from focusing on the target to immediately switching to focusing on the front sight with the handgun is where I am having problems.
Guess I need to practice more with this transition.
Any tips?

You said it already, more practice.  You need to practice to the point the transition is second nature.  It won't take as long as you might think.  Creating those paths in your brain is pretty quick.