Ok so I made some more progress this weekend. Shifter, clutch, and clutch pedal are installed. I'm not going to do a total DIY as some of the information is readily available online as DIYs such as how to remove the DSG, how to remove/install shifter, how to change the clutch, and how to reinstall a manual trans after clutch change. I will note some things specific to the swap and some shortcuts I have found in regards to the above DIYs.
1. To remove the DSG you DO NOT need to shift the engine forward, shift/pull the radiator, or drop the subframe as some manuals and online tutorials describe. Simply remove the drive axle flanges from the DSG and it will easily go out the bottom.
2. After removing the 6 M12 bolts from the DMF it still did not want to come off the crankshaft even with pulling and prying. I had to tap the sides of it with a hammer in a circular pattern to break it free.
3.The shifter was the biggest pain so far in the swap. The 4 nuts that hold it in place are in the cabin and it drops out of the bottom. It would be much easier to swap the shifter with a lift. Optimally you would unbolt the exhaust at both the turbo and the clamp before the catalytic converter and then remove the headshield. The clamp at the turbo was giving me trouble so I unclamped the exhaust before the cat and was able to scoot it over enough to bend the heatshield and swap the shifter. I don't recommend this route because it's going to be difficult to straighten up the heatshield due to how much I had to bend it.
4. The automatic had the access hole already in the firewall along with the studs to install the clutch pedal. There is a plastic plug that pops right out of the firewall. Even the sound deadening in the cabin was already perforated for the clutch pedal. No cutting was required.
5. The brake pedals ARE DIFFERENT between the automatic and manual. You will need a brake pedal from a manual trans car.
At this point I still need to install the trans and axles, button everything up, bleed the clutch, and then do the wiring and coding of the ECU.
Picture of clutch pedal installed and also differences in brake pedals. The uninstalled pedal in this pic is a brake pedal from a manual trans car. A special tool is required to remove the clip that holds the rod/ball from the brake booster to the brake pedal. I was able to use two small screwdrivers on each side of the clip to remove it without the special tool. Also note that if your car is built after Nov 2005 you will not need to swap over the brake switch as it is mounted on the master cylinder. Cars built before that had the brake switch on the brake pedal.
Perforated sound deadening material and plug from firewall for clutch pedal.
Clutch pedal access hole is directly next to the brake booster. The brake master cylinders appear to be the same between automatic and manual. Just cut off the nipple on the side of the master cylinder reservoir and run the hose to the clutch pedal master cylinder.