Are there any removal and replacement issues that I should look out for?
As usual Lars advice is right on.
If you read your 66 Shop Manual about removing/replacing exhaust manifolds you will see that it says the engine is first to be removed from the car! I can tell you from experience that it is certainly a whole lot easier to remove the manifolds that way but it is not necessary. Besides, removing and replacing the engine (and transmission with it) obviously makes the overall job a lot more difficult and time consuming. I replaced the LEFT side exh. manifold on my 66 after getting everything out of the way first including removal of the power steering hoses. Then I proceeded to break off at least a couple of bolts (it was awhile ago), fortunately (?) they broke off leaving plenty of shank left once the old manifold was finally off. Vice grips, PB Blaster, and time got the broken bolts out without pulling the heads. For me, it was a MISERABLE job, but it got done, I dont envy you.