-install the nylon snap ring
http://home.comcast.net/~mmunoz70/z/csts07.jpg
-install the metal snap ring. You may need to tap it down a bit to seat it better. You may not be able to seat it fully, but that's ok.
-lubricate the top boot with light oil then slide it down the shifter shaft. Work it back over the shifter base ring.
http://home.comcast.net/~mmunoz70/z/csts08.jpg
-go underneath the car and apply a glob of lithium grease to both sides of the shifter. This will aid in holding the brass or nylon bushings in place as you slip the shifter linkage over the base of the shifter. You should select a bushing that is about as thick as a penny or at most as thick as a nickel. Use one bushing on each side of the shifter base.
http://home.comcast.net/~mmunoz70/z/csts09.jpg (this pic shows the bushings above the penny that come with the STS meant for the Civic, the bushings below I picked up at Ace Hardware for $0.65 each)
http://home.comcast.net/~mmunoz70/z/csts10.jpg (in this pic the very thick bushing is the bushing that came with the Civic STS...the penny and the brass Ace Hardware bushing are about the same)
(Upon further evalution, the bushing should be as small as the one that came with the Civic STS with regards to diameter. Alternatively, use a nylon washer of larger diameter)
-reinstall the linkage nut and bolt. Tighten the fasteners securely, but do not overtighten as this may cause some binding and notchiness of the shifting. If there is too much play in the shifting tighten the fasteners more. If it's too notchy, loosen them a bit.
-reinstall the center console and wiring harnesses
-reinstall the shifter grip
http://home.comcast.net/~mmunoz70/z/csts11.jpg (Double bend Civic STS as it sits in the PGT)
That's it! You are done.