Check timing and do a compression test First. Are you using the correct ecu for the engine ?
They are torque less engines , only fast in vtec just to its small displacement but if you're saying your old b16 felt faster which is around 30hp less than the b16b then something must be wrong, I doubt the cracked HT lead would cause a drastic power drop, probably a slight misfire occasionally.
also was the engine purchased off a reputable person ? If not I'd take the rocker cover off and identify the cams , since ek9 cams are sought after I wouldn't be surprised if they've been swapped out.
From memory ek9 cams have 2 rings on the end.
Believe compression should be around 250psi or higher but don't quote me on that.