What have you ran in the 1/4 mile??

My friends got a B20 (JDM) in his 89 CRX and he ran a 13.2 on street tires with filter on the end of the TB, header, header-back exhaust, FPR and 255lph pump.
Hes got nothing but bottom end, i think its the VTEC head that got rid of your bottom end. The stock B20 and B18 have bottom end cause because of their bad headflow. With that VTEC head the headflow is increased a lot and thats where your torque went. At least thats my theory??

My friend is useing the LS ECU, i guess thats why he cant rev past 6800rpm. He now has a ported/polished, bored over, 3angle valve job.............all that fun stuff.

Since you have a VTEC head i think that mugen ECU is fine. It might be running a little rich from idle to when the VTEC kicks in. That also might be where your bottom end has gone. It might be running too rich in the lower rpms making the engine bog.