I too am in the same situation. I have a LQ4 out of a 2004 GMC Yukon XL that my buddy is installing into my 94' 2dr Blazer. I'm most likely going to upgrade to the 4l80e as well.

According to the guys at Street & Performance (http://www.hotrodlane.cc/):
While on the subject of transmissions, it should be known that
‘94 and earlier 4L60E transmissions used a 12 pin connector
and can not be controlled by the GEN III computer, only ‘95
and Later 4L60E transmissions using 13 pin connecter can be
used.