[projectRDM]

Why did you bother using a manual lower harness? The auto would have had all you needed for starter, alternator, VSS, and OPS, then you just hardwire the reverse lights if you want them. Done.

But to answer your questions, number #1 in pic #1 is the starter plug, auto cars have that plug for the starter inhibit, just tie them together. Number #2 is indeed the electric fan.
In pic #2 the plug with four leads is alternator signal, OPS, and VSS. The 6pin plug is for the transmission switches I believe, the majority of which you don't have in the chassis harness. Nor do you need them.