The thinner the layer of AS2, the better your conductivity will be, but that is really dependent on how flat flat the bottom of your HSF is. Here's a quick guide to lapping, but if you run a search there's a link somewhere to a good guide, or you can just run a search on yahoo and it should give some links. Here's what you'll need:
1) Sandpaper, silicon carbide. I just got the variety pack, it had different grade grits from Coarse to fine.
2) A small piece of glass (palm-sized) or a flat/stable table or work surface.
3) Some water.
4) Acetone or Isopropyl if you don't already have some.
Basically, lapping is just the process of evening out the surface of your HSF as well as getting rid of any of the dings which can create valley's and air bubbles between your cpu and HSF. A lot of HSF's are not perfectly flat, and lapping can solve a lot of bad contact problems.
Take the fan off before you start lapping. Just wet the highest (coarsest) grade sandpaper, set it on the flat surface, or if using a piece of glass, wrap the sandpaper around it, and get to work in a circular or figure 8 motion on the bottom of the HSF. The coarsest grade will give you some thick grooves on the bottom, but don't worry, this is just to get those really deep dings and scratches out of the bottom. Switch to the next finer grade, wet, and repeat. Switch to the finest grade, and repeat again. I spent the longest time with the finest grade, I didn't get a completely mirror finish, but as long as the lines caused by the sandpaper are the only lines or dings you see, you're fine. There was a *huge* difference in my HSF's uniform smoothness after I lapped it, and the temps I got before and after convinced me this was something well worth doing. It gets kinda messy, so you will want to run your Heatsink under some water and scrub it a bit. You can dry it with a blow dryer or let it sit overnight. I actually tossed it in my oven upside down for 10 mins. under like 150 F. Clean the bottom again with acetone/isopropyl. The best thing is that you need a much thinner layer of AS2 now that you know your HSF is flat and is pit-free. You will still want to put some on the bottom of the HSF and buff it off like the AS site says, and apply a translucent layer on your cpu core.
Also, with the Golden Gate, the best way I found to put it back on, was to pull the side w/out the clip as far in as you can get, gently attach it...sit the heatsink down on the processor, then press the clip down with both thumbs. It doesn't shift around at all, so you know you have a good contact. Hope this helps.
Chiz