What is better?

you'll get more cornering stabilty but then the downside of stock stocks is the plush ride you would get from an aftermarket shock. So it all depends on which you would rather have.
 
no like with the yfz shocks. you wouldnt have to same kinda ride you would with the works shocks. you will just have more corneing ability with the yfz's. But are the works shocks the length needed for the +3 arms or for the stock a arms?
 
I will either get +3 long travel with YFZ shocks or +3 std travel with the proper works shocks. I'm thinking the yfz's will be the better deal.
 
A-arm travel is limited to a practical amount of about 10" (more if you're willing to change a few design parameters like having your quad be 6 feet wide) no matter what shock absorber you are using.

The trick with aftermarket shocks is they can tailored specifically to your weight and riding style. If you take a set of shocks tailored perfectly to your weight and riding style and stick them on extended a-arms, they'll be too soft and not control the travel very well.

The advantage of the YFZ shocks is that they are a little easier choice... and usually less expensive. You can get YFZ shocks revalved and even resprung but usually they are adequate in their stock form.