hi dodgedude,
i had a "new" (5k miles on it when i got it) 68 barracuda formula S in high school and the plymouth mechanic that i bought it from had put hooker fender well headers on it. chassis headers will add around 25-35 horses to a 340 and fender well headers add more like 50 hp - 340 like to "breath."
i just restored an exact duplicate of the car i had in 1969 - except it doesn't have fender well headers - just under chassis. it's an original S car and i could not bring myself to cut up the factory fender wells. if you're going to race, then you have to max out all the performance mods on the car and that means you have to go the fender well header route. however, if serious racing is not what you're doing, i would seriously reconsider cutting up your fender wells. if you ever sell your car cutting those holes will probably take $2-3k off the sales price.
if you do cut out the fender wells, do it as carefully as you can and save all the metal! you can at least give all that to the next buyer in a box and tell him the car can be put back to stock.
good luck which ever way you go.