The simplest rule is to do exactly what the spell says. You gain the form of the large animal, you gain the exact amount of STR and AC and lose the exact amount of DEX as described in the spell description. This would be RAW since the spell makes no exception for small vs. medium casters.
The slightly more precise rule is to also remember that you have certain modifications for being small and to remove those modifiers because you are not small anymore. This is also RAW; the spell doesn't instruct you to do this, but the description of "Polymorph" spells says you should: "If a polymorph spell causes you to change size, apply the size modifiers appropriately...changing your armor class, attack bonus, Combat Maneuver Bonus, and Stealth skill modifiers".
So, by RAW, you should do those two things.
I would suggest creating a few 3x5 cards that list every modifier you get when you change to tiny, medium, and large size. Then you don't have to do tons of math every time you cast one of these spells.
To add to DM_Blake's post, you should change your size modifiers from those for small (+1 AC/Attack, -1 CMB/CMD, +4 Stealth) to those for large (-1 AC/Attack, +1 CMB/CMD, -4 Stealth).
You definitely *do* change to Large size, not just to medium. Even a diminutive creature affected by Beast Shape II would grow to Large size. However, for any creature that is not originally small or medium, they get additional adjustments to their physical scores before applying the polymorph affect (see the Polymorph subschool of Transmutation in the Magic chapter for details if you happen to have this happen - doesn't normally happen to PCs).