civiclxb16a

ok here is the deal i got my b16 in and running but i noticed that the lights are dim and after about 10 or 20 mins running the engine starts bogging down. i put a batter charger on that i have and the lights get bright and the engine runs perfect. now on the altenator there was a different plug then what my civic has. i have a 97 civic and the engine is a jdm obd1 b16a2. i took the plug from the obd1 wiring harness and put it on my stock obd2a harness but could i have done something wrong there i matched the wire colors from my stock harness to the new plug and the one on the top was the same as my stock harness! what could i look at or do to get this problem fixed? can i run a wire from the alt right to the battery? please let me know guys thanks