Just picked up a set of Koni SA for my 95 Z28 from Summit. The didn't come with bolts for the bottom, instructions or any kind of diagram. I got a bag of 4 rubber bushings, 4 fine thread bolts and few washer looking things. I'm guessing the rubber bushings go on top one under the body and one Inside the car. Does anyone have a diagram on how these things so I can check assembly and check for other missing parts. My google search landed me nothing.

 

Here is the Koni adjustment page. You should be able to score a phone number or contact info on here:

Koni North America - ITT - Adjustment

 

You're right about the top end order on the threaded rod -big washer-rubber-through car sheet metal -rubber-washer-nut. The bottom should mount the same as yours are currently mounted.
The instructions I got with my shocks were like a retard wrote them. All torn and bouncing around in the box which was also all torn up by the time I got it. I couldn't believe how bad they really were.

 

The bottoms on my old ones has a metal type spacer. The koni doesnt have any spacer with it. I'm guessing the nut acts as spacer.

 

Front and rear install and adjustment instructions

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Just make sure the bushing housing or the bottom raduis of the shock body doesn't contact the mount in any way other than where it is mounted through the rubber bushing. It needs to have a little space there and needs to be isolated from metal-to-metal contact so don't be afraid to improvise a little if you have to.