There are different, separate harnesses for different parts / areas of
the car.

I assume you are talking about replacing the harness in the engine
compartment?

Most especially the harness which is under the intake manifold, and
which goes under the front of the block?

This harness wears out first, and failure is endemic.

I  replaced mine.

I sourced the replacement in a U Pull It yard; the prior owner seemed
to have replaced his recently, it seemed nearly new (nice find).

I removed the intake manifold, and with that off, it was pretty
simple.

Just an exercise in logic, really.

Ok, I got most of it in, just some fine tuning of the connections,
etc...but I have a few questions.

There are two male connections on the engine block, one is higher than
the other. I'm pretty certain that I connected it right, but I was
unable to label it properly.

What goes to it?

Also, there's a 3 prong connector thing (much like the ones that
connect into the manifold), but I don't know where it goes. It was the
only one I didn't label, and stupidly I didn't figure I needed to. Or
maybe it's an extra one (? that doesn't sound right).

It has a blue ring around the end of it, if that helps.

Does anyone have a diagram showing what goes to what (thats easily
readable)?