Well some of my headaches with wiring have been solved. Partly me being blind and/or asking the right folks and google.
Anyway, i figured out the connector below is the GBCM connector. GBCM (Generator Battery Control Module) - PCM controls when the alternator comes on/off for fuel efficiancy. This can easily be identified by the 2 red/white wires that go to C2-D5....and the grey/brown wire going to the alternator. This connector is not needed. On LT1swap's chart, you take the grey and brown wire and go directly to the PCM. It is highlighted in green.
I was going about it the wrong way. I was trying to find out what the 2 red/white wires were for. Next step was to check other wires....bam thats the alternator connector. Don't you hate it when you give yourself a headache for no reason!
After reading up on coil relays and protection for them, I noticed the fan relay box that came with the engine/harness. The relays have a resistor across the coil, so it appears the manufacturer built those into the relay. It may be a varistor (decreases resistance as voltage goes over a threshold...this would be better than a resistor). The box is built and the relays work, why not use it.
Now I need to find pigtails for the 98 Windstar fan. I can find a 3 pin for $17, but can't find the 2 pin for the other fan. I'll be damned if I'm gonna pay $30 for 2 connectors, I'll figure something out (used or build one myself with Plasti-Pair).
Also decided to remove the Neutral safety switch/wiring and use whats on the vehicle. Thanks to Doug and Foamy for their help on this one. Why double up on ckt's when one will do....less to go wrong during install or later down the road.