couldnt you just put a thin metal rod into one of the spark plug holes? turn the crank by hand till the piston hits tdc, mark the rod, then rotate the crank till the piston stops going down. mark again. pull the rod out and measure the stroke

 

5.4" rods, you should see some sort of clearancing in the cylinder skirts for the rod bolts

 

I think if you have a 331 you should use the 'fast as cast' TFS 190cc heads, it's easy to get a head thats too big.....
BTW, I'd also ditch that cam, Comp cams has much better.....