Wiring bundle question

[yale]

After swapping out my 7MGE with another one I have two electric connectors that remain unidentified. The engine swap was short block so all the harnesses and components were reused. It is an automatic.
The first is a bundle of five (5) brown and brown/white that are all part of single loop. Very much like a ground connection. These come down through the intake plenum and reach down towards the starter area. I believe they are ground and connect with a bolt on the plenum.
The second is an electrical connector, square and grey/clear, that appears to go with the three large transmission connectors, again down by the starter.

The starter will not engage but I believe that we have one of two issues there. 1) neutral safety switch or 2) security system (but I don't have the Theft Deterrent Computer in the car anymore).

Any help on identifying those electrical connections would be appreciated.