I used a generic harness with the 20 mini fuses and was able to install it close to the original location. It sounds like you are going to have a lot of leftover wires... Are you going to pare it down some? It's amazing how all those extra wires take up space when you don't have any need for them.
The Painless manuals are pretty good for highlighting things that aren't covered in the original schematics.
http://www.painlesswiring.com/Manuals/20120.pdfAs for as weatherpack connectors, about the only place I think I should have used them is on the front parking lights and the backup light. Otherwise, just about everything else had a factory style connector that is weatherized from what I recall.
On the firewall, I placed holes on both ends to feed wires to the respective side of the engine compartment to minimize wires spanning across the bay. On my chebby, I added a 3rd hole close to the bellhousing to run the starter solenoid wire, oil pressure line, temp sensor wire, choke power and ignition power.
One thing I did that worked out well is I had a full chassis harness from an '89 mustang and from that I cut every pair of male / female connector with about 12" of wire so that I could make cleaner splits. I suppose thats what you plan for the weatherpack connectors, but these were free to me and usually the pick and pull will only charge a buck or two if you need more.
Are you using a stock column or a replacement that uses the stock GM connector... the bonus there is you get to take advantage easily adding hazard lights.