I have a 1966 Mustang, originally a 200 ci. I've been told the six
cylinder Mustang bodies were not as strong/stiff as the eight cylinder
Mustang bodies, and while an eight cylinder engine does fit into the
engine bay, it will put more strain on the body due to the extra
weight than the original six cylinder body was designed to take. Were
eight cylinder classic Mustang bodies more reinforced than six
cylinder bodies?

Maybe, but ??The 1960's Mustang was an awful car then, and it's even
worse now. It was a lousy Ford Falcon with a different body. It rode
terribly, handled terribly, braked terribly. So what did Ford do to
improve it other than slap a racier body on it? It put a bigger engine
in it!? from http://www.cartalk.com/content/columns/Archive/2003/February/08.html

Hello.

I'm not 100% sure of this, but from my reading, an 8 cylinder 65 & 66
Mustang have 1) 5 lug brake drums as opposed to 4 lug on the 6
cylinder, and 2) heavier coil springs in the front to support the
extra weight.   I believe that is the only "structural" difference. 
:)  Good luck!

In addition to the other comments when making the switch from the
6-cylinder to the 8-cylinder engine you will also need to update the
brake system, larger spindles for the front wheels and should also
switch out the 8-inch rear end for the 9-inch. Some other tricks that
you may want to do is to beef up the shock towers for added strength.
The 8-cylinder engine, such as the 289, will fit into the engine bay
but there are a number of modifications that need to be made to go
with the larger engine. The 6-cylinder also used a single exhaust
system instead of the dual type used on most of the 8-cylinder cars.
Even those of us who have the 6-cylinder variety have improved the
handling and braking of those cars with minor modifications.