I have the steps that I actually took to do this listed below. I think there is probably room for improvement and many ways to accomplish the same end result depending on whatever strong skills you may have or what tools you happen to have. Not every step has a picture associated with it because either I couldn't hold a camera and do it at the same time or it just wasn't worth it to photograph a mundane task like tracing a line.
Also, keep in mind I was doing this for a GSM nexus. I can test whether an LTE nexus (both standard & extended battery) will charge in the dock sometime on Tuesday or Wednesday.
Tools & materials used are described throughout. After the steps/pictures I have some concluding thoughts including some lessons learned, things I would do differently, and some alternate ideas others might wish to consider.
DISCLAIMER: Bad photography ahead.
Step 1: Grab a good beer, somehow these things always take longer than you expect.
Step 2: Tape the phone & dock where you will be measuring with a caliper or holding it in a vise. I used masking tape which turned out to have the extra benefit of being able to see the contact points through it. Take a lot of measurements. You end up drilling the dock blindly so your results all start in how carefully you measure things. Don't use the numbers on my caliper for your own use... Somewhere around the time of these pictures I accidently zeroed the caliper so I don't know which ones are showing correct values or not. I only realized this because I measured everything again and realized something wasn't right with the numbers.
Step 3: Double check your measurements, make sure everything is square... I want to say the following picture is over board on my part... but it really is a fine line between making contact b/w the pins and the phone 100% of the time, 50% of the time, or hardly ever.
Step 4: I used a pencil to trace a line from the contacts up the side of the phone, and onto the front glass. I then place the phone in the dock and put a new piece of tape from the edge of the phone around the edge of the dock and traced the line back over the dock so that I had a good reference for where to drill in the side-to-side dimension. The vertical dimension was purely based off my measurement from the face of the phone down to the contact points. Because the glass is curved, take separate measurements for each pin.
Step 5: At this point I used a 1/16" drill bit to make two holes and then pushed the pogo pins through. Before proceeding I hooked up 5V power using aligator clips to the pins and put the phone in the dock just to make sure everything was in the right place before I really made anything permanent. In this picture the pins are only held in place by friction. The dock is very rubbery at this location which is nice for holding the pins in place. You can see how well you lined up the holes by placing the phone in the dock and looking through the holes. You absolutely want to see the entire gold contact nicely centered in there. If not, fix things now before proceeding.
Step 6: I then took a car charger and cut the micro USB end off. There really isn't much to picture here. I happened to use a car charger with a permanently attached cord so there were no data wires. If you use a USB cord that contains 4 wires, usually red, green, white, and black, just tape off the green and white (date + & data -), and use the red (+ 5V DC) and black (ground). The pogo pin closest to the power button is the ground and the pin closest to the bottom is for 5V (I confirmed this for both the LTE & GSM models). Middle pin, assuming the same paradigm used for the nexus one, is for signaling the type of dock and the bluetooth id of the dock.
Step 7: I soldered the 5V and GND wires to the pins as described, sealed some exposed conductor with heat shrink, and used an epoxy to permanently seal them in place. You want to make sure you use an epoxy that bonds plastic and I would also recommend one that advertises some level of flex/gel. If it's too rigid or poorly bonded to plastic you could end up cracking off on the very first insertion. Make absolutely sure that the pogo pin plunger is the only part of the pogo pin that is on the inside of the dock. Even a small portion of the rigid part will cause you problems when you push the phone in and it pops the pins back out or damages the epoxy.
So, did it work...
After waiting enough time for the epoxy to set I got what I had hoped for.
I also added an NFC tag to the inside that I'm using to turn on bluetooth, set car mode, etc, etc...
Here's a few extra pics:
It successfully charges my GSM nexus with both the standard and extended battery. It would appear to me that the dock holds the phone with the position of the front glass relative to the lip of the dock in a constant position. So I'm assuming my wife's LTE nexus will be able to charge on the dock as well (will test on Tuesday/Wednesday). That would be really good news for VZW people who aren't up to the modification but would like to buy the GSM dock if it ever comes to market. At this point at least, it can concluded that it's possible to make a dock that charges the GSM model with both the standard and extended battery with the pogo pins in a fixed position.
Now that it's been done once the thing that would make this an extremely fast and easy mod in my mind would be a drill guide jig. An L-shaped jig with drill guide holes that you simple place against a reference point on the dock and drill in the holes and never have to worry about all that measuring and how well you measure.
I also wish I hadn't soldered the pins to a fixed car charger. Now I'm tied to that thing unless I want to cut the cord and splice a new USB plug on the end. In hindsight I actually wish I had used a 2 conductor "boot" close to the pogo pins that would allow me change the cord easy and provide some level of emergency strain relief or break-free ability if the cord were to get yanked. On the topic of strain relief, this is why I recommend right angle leads off the pogo pins. It also might be a good idea to adhere the cord to a spot on the back of the part that holds the phone so that a snap tug on the cord pulls on that and not your pogo pin connection. It feels very durable and I don't expect any problems it's just something I would recommend.
As for the NFC tag, I would use the thin adhesive tags, you don't want anything thick enough to change the contact position. I used a 1K tag so that there was plenty of storage for long instructions/information that may be handy to write to it. Right now it just launches car home, maxes the media volume, starts bluetooth, turns off wifi, and sets a high brightness level.
Finally, I wish I had gone ahead and installed a middle pogo pin with a free hanging wire lead off of it. Just in case I felt up to going down that rabbit hole in the future. I wish I still had a nexus one dock around to see if the signal pin on those docks would communicate on the galaxy nexus middle pin. I know, different OEMs (HTC) but the code is Google's so I figure there's a 50/50 chance it actually would work.
Your move, Samsung.