sorry for the delayed response...
first, skunk2 is a great company, but i wouldnt call them the best... it is wise to match valvetrain parts with the same company to help eliminate any variances in manufacturing different companies might have.
as for tranny choices, that would greatly depend on what you will be using the car for..
if all you care about is acceleration, i would suggest the b16 trans.. if you drive on the highway a lot, the LS trans... and if you want a middle of the road, the GSR Trans.