"I had my linc 430 rebuilt (.60 over, isky solid cam .505 lift, roller lifters,rockers, custom pushrods, msd ignition box, holley 750 cfm)and now need exhaust."

DAMN!
"Is the stock 2" too small? Would 2 1/2 " exhaust be worth the extra money?($ 450)"
I think it is. Much too constrictive for all you have done. 2 1/2" from the exhaust manifolds to the mufflers at least (resonators removed?). If I am correct here, the OEM crossover is before the resonators? I would have the fabricator move the crossover (I would consider a pre-fab crossover) to the point of the inlet pipes where it will offer the most complete balance. If it is a HI-PERF shop, he will know what you want or I can detail it for you.
You only need 2" outlets (after the mufflers) as the exhaust gas condenses at this point and the larger tubes are not needed unless you want the visual effect.
"Another question , low vacuum (7") with the new cam give some serious hard pedal pressure to stop, not to mention trans shift issues."
Quite a cam. How's the driveability?
A vacuum assist needs at a minimum 16" of vacuum to operate properly. If you cannot raise manifold vacuum with timing adjustment, etc., you might want to consider either an accessory vacuum pump or maybe going to HYDRO-BOOST. How correct do you want the engine compartment to appear?
The actual shifting of the trans is controlled directly by the modulator valve and it needs to operate directly off manifold vacuum. If this low, you will experience shifting problems. I can refer you to a trans man who understands the COM. He may have a suggestion or two.
"Initial timing is another question, how much is too much, idle(now at 12 btdc), 2000 rpm (30 btdc), any suggestions?"
Did you recurve the distributor advance or leave it alone? Did you keep the vacuum advance feature? Are you absolutely sure there is no vacuum leak on the engine?