Will I get real time cornering clearance by going to a 12.5" or 13" shock? I'm riding a box stock 05 FXDL.

 

Remember that the angle of the shock means that you don't get a one for one increase in "lift" for length. I went from 12.5" stock FXD shocks to 13.5" (roughly) and it only raised my bike's frame by about .7". I'm going to dial in another half inch of length and see what I get in the way of ground clearance....but I'll do this after I get new tires on it tomorrow.
Even the relatively small amount of lift made a noticeable difference in cornering clearance and nimbleness. I also lowered the fork units by about a half inch in the yokes. I'll likely bring them up to flush again with the longer shocks.

 

I put 1/2" longer than stock on my 02 wg and it all but eliminated the drag in corners, and, made the ride a bunnnnnnch better

 

Went a half inch longer than the 12" stockers and found a real improvement in cornering clearance. It's also more comfy without being soft.

 

i went with the 11 inch prog, because of the lowering ride is harsh does anyone know of a shock that is 11 in but gives some comfort

 

If you run a short shock, it will have very little travel. To keep from bottoming the shock, these use very high spring rates. There is no way around physics. Short shocks will be harsher than longer shocks. You will get incremental improvements with fully adjustable shocks, but I don't think you'll feel you got your money's worth.
I can't see the bike when I'm sitting on it and honking through corners, so I don't give a rip about "looks" when it comes to something so fundamental to my comfort, safety, and enjoyment as handling and suspension.