Will you be installing this D16z6? Or a shop?
You should use the matching transmission due to the gear ratio being better matched to the engine. Drive shafts should be taken from the z6 as well, better matched for the extra power...lol. You will need to wire your car up for VTEC-E as well and get a ECU for the D16z6 too.
Look, if your going to pay a shop to install this "engine" you might as well pick up a B16 and not a D16...If you are thinking putting a turbo in a D16, you will need to get stronger rods and your transmission will not last very long, they are weak transmissions for any extra power over oem. Same for the drive shafts, they too will need to be upgraded to handle more power. D16's are economy engines, not performance engines; more fragile than the B engines.
I have had d16's in the past, built them up fully and still could not keep it running due to everything becoming weak for the power it was generating. I upgraded to a b16, and now to the b18c-r. My time spent building up the D16 only taught me to never build up a D16 ever again, its a waste of money.