cammerfe
Dedicated LVC Member
It seems that the LS doesn't play well with aftermarket alternators, and that may all or most of your problem now. The problem before was very likely to be a bad connection of the alternator feed back wire to the PCM.
Here's trouble shooting for that problem.
http://deneau.info/ls/s6x~us~en~file=s6xe0003.htm~gen~ref.htm#PS2-D
One more time Joe, "You the MAN!"
KS