The project isn't 100% finished, but its fully functional. All I need to do now is make it look prettier, IF ANYONE KNOWS OF SOME FORM OF PAINT OR FINISHER THAT RESEMBLES SOFT-TOUCH RUBBER PLEASE LET ME KNOW.
Basically all I did was take some 220 grit sandpaper to it, then followed up with some 400 grit to smooth it out. The process took me quite a while because every time I would finish it with the 400 grit the phone would once again start sliding up and lose connection with the pins. I found that you will either need to remove quite a lot of material, or leave the surface relatively rough so that it grips the phone and holds it in place. I initially started with some 100 grit paper, but you have to be very careful as this will gouge the plastic pretty bad. You can smooth it out, but it will take a lot of work. If I did it again I'd start with some 180 grit or so for the primary material removal, then smooth it out with some 250 or 300 grit.
I left the phone all night in the dock and it did not lose connection. I have had it in the dock all morning, with some light use, and the connection hasn't been lost. I am running AOKP B37 and the phone immediately launches the clock app and begins charging when I place it in the dock. Also, the phone charges at AC rate when the dock is connected to a wall outlet. I haven't tested when connected to my PC via USB. Data transfer doesn't work over the Pogo Pins anyway so there isn't really any point to connect it to your PC. AUDIO OUT VIA A PAIR OF CHEAP PC SPEAKERS WORKS FLAWLESSLY, IT IS NOT USING BLUETOOTH.
I initially tried sanding down only the side to the left of the pogo pins, where the bottom of the phone rests. Unfortunately this did not work, I had to remove some material down the entire length of the dock. I also found it very important to sand down the inside edges of the front ridge running along the bottom and sides. Its relatively easy to remove a decent amount of material from these sides, and will help the phone rest on the pogo pins. I also remove a good amount of material from the 'groove' where the top and bottom of the phone slide in.
Its not the prettiest thing right now, but it is functional and I think with a little more sanding and the proper paint I'll be able make it look almost like new.
If you're like me and love having a dock on your desk, don't be afraid to try this out! Its very easy and as long as you don't mind the dock looking a little scuffed.