Wow, what an epic (and long) read.
We bought a 2011 GSW in the summer with ~110k (70 000 miles) and while I haven't experienced a hard start yet, I have seen some pre-warmed up shuddering under power during our fall mornings. This is my first diesel but I think I'm sold, the torque is invigorating (my VW passion runs deep though, my last 4 daily drivers have been been VWs/Audis - an a3 Jetta, B5 passat wagon, C5 Allroad and an 88 Scirocco that I played with for 5 months this summer while I looked for a replacement for our Allroad, amazing how much you'll put up with once the VW bug bites).
I also had a odd event in September that is likely also related to condensation in the intercooler - I took two of my kids on a day trip out to see the columbia ice fields. There was no snow (or rain) that day, but temperatures ranged from just under freezing for the drive out, to around 30-40F for most of the drive back until just after supper time when the temperatures were probably in the mid 40's up into the mid 50's for the last hour of the trip (i.e. cool but sunny for most of the day's driving, but warming up as I got away from the mountains). Driving a stretch of two lane highway, dropped into 5th gear to pass the stacked up cars and trucks when a passing lane came up but had a stumble and what felt like a plugged inlet. Since I had started reading this thread by then and had my own theories about what was going on, I dropped another gear and proceeded to ramp up the RPMs thinking that I had to clear the inlet out. Seemed to work good, but after another hour of cruising in 6th gear, when I got off the highway to take the back roads into our neighbourhood I had the same thing happen again. Again, I ran a couple of gears long and tried to clear out the intake. Looking back, I'd characterize the trip as mostly loafing along in 6th gear under load (hilly mountainous terrain), interspersed with 4th gear passing up until the last 2 hours of the return trip which was mostly 6th gear loafing with low load - sounds like optimum conditions to frost up the intercooler, then melt it off as the temperatures rose near the end of the day.
I'll add my own theory about why the intercooler retrofits seem to help some people for a year or two (and similarly when new cars weren't typically a problem) - I'm wondering if a clean intercooler has less issues with allowing the condensation a location to attach to the walls of the intercooler. In other words the oil/goop that builds up on the walls of the intercooler are now initiation sites for frost or ice to build up during driving which increases the amount of condensation that is not flowed through the engine (whether as droplets, or in vapour form) during high humidity events, but instead its banked in the intercooler until you stop/park and either ambient conditions or the engine heat melts it and it collects at the low point. Intercooler cleaning isn't an easy thing to try (and I know typically the reason to clean any cooling device is to remove the fouling which acts as insulation and return the cooler back to initial efficiency, which runs counter to the theory that these intercoolers are too efficient which causes them to freeze off) so I doubt anyone would want to test this on their own car.
Second question - I wonder if the cheat programming made it impossible for the LP EGR to work properly (probably, since its purpose was to manage NOx emissions, maybe the LP EGR valve programming was trying to accomplish the NOx targets while the other programming was ignoring the high NOx levels).
As for my car, I'll likely put it up on the ramps and drill a 1/32-1/6" hole so it can drain, I'm in the process of making up my own winter covers for the lower and upper grills (it was only $25 for -75C PVC cloth, now I just have to get my kids to teach me how to run their sewing machines

) and when finances permit there will definitely be a Malone tune, possibly with off-road modifications. I'm curious that there weren't more Calgarians with issues - our temperatures are all over the map when chinooks and winter storms blow in. The coldest weather definitely knocks the humidity out of the air, but the winter storms are usually right around freezing, then a chinook blows in and melts it all off again (over and over and over again through the winter and well into April/May). Temperatures can range from -20C in the morning to well above 10-15C in the afternoon as a chinook rolls in.
John