charging issues on genIII swap

i had done a search but still have questions, i didn't want to jack other threads so i started this..06 hemi and alt. in 68 barracuda. megasquirt EM
every single wire/plug are brand new. i am using an external regulator. its a 68 single wire configuration. it is the modern electronic version.
i grounded one of the field wires on the alternator. the other field i ran to the new regulator.
i have the keyed wire from my brake light switch powering the regulator. i have a 4gauge wire straight from the alternator to the hot side of my ford starter solenoid, the fuse box is powered to the hot side of the solenoid too. everything works as it should,
BUT all my lights flicker
and if i unplug the keyed wire from the reg. the engine runs better and lights stop flikering
WHY?????