Faster acceleration or top speed? If they're both stock gearing...all the mods in the world won't help the 400ex because its not geared to go as fast as the z400 will. Assuming the same riders and conditions for both, the z400 should be FASTER....however the ACCELERATION of the 400ex with pipe and jets "might" be as quick or quicker than the z400.
I owned a 2000 400ex with timing advance key, billet end cap, dynojets, uni filter, 22" Bandit XT rears, and 14t front sprocket and it was still slower than my stock 2003 z400.
GPS verified top speed on the 400ex was about 62 mph. GPS verified on my z400 is 67+. I got 69.5 down hill and 67 on the flat.
"He who dies with the most toys, wins"