Rta 3 is all tar. Dull, mostly flat, but if not windy, nice and quick. Rta 40 is subject to lots of roadbuilding lately by the sound of it (I was last there 3 years ago) gravel, dust, slippery when wet (but not boggy, normally!) much better scenery and ultimately much more rewarding. Is gravel softer to fall on than tar when you're blown off a bike?
Are you going south and north or 1 way (jumping off TdFuego?) I'd at least attempt rta 40. If the weather turns on you the distance to the east coast road is not great...