Of course a transmission cooler instructions are going to give you the recommendation that will give you the most cooling, though to be technically correct their cooler will work the most efficiently when mounted where it gets the hottest inlet temperatures.
It doesn't matter...
the fact is that if you read what they wrote, that you want to maintain transmission temps of 160-200* (very close to what I suggested) and that you'll get double the fluid life at 175 that you will at 200 (which is the reason that I suggested 160-180), then if you have a sufficient cooling system which has a typical 160* thermostat, my suggestion of mounting the auxiliary/external cooler before the radiator cooler will keep the transmission fluid temp in the correct range the largest percentage of the time.
The only time I would do it their way is on a hot running engine, and even then I would be looking for how to cool that down, since an engine running hot enough to need this will not be making best power.
I've never used shims on a converter but, I'm not an auto transmission expert either. The only reason I can think of to do that is to get proper converter to pump engagement correct. If that is the case I'd assume the shims would go between the converter mounting studs and the flex plate.
I didn't say anything about this because I could see how this would change from transmission to transmission and converter to converter and most of my experience is with GM transmissions. That said, I usually eyeball it: get the converter fully seated in the pump and then get the bellhousing bolted down, a
t that point I hope to see (and always have seen) ~1/8" (maybe 1/16-3/16") between the converter and the flex plate. If it was right up against it, or more than about 1/4" I'd be concerned something was wrong. I've seen it right up against the flexplate (usually newer converters with lockup), where the converter was not properly seated before the transmission was installed, but I've never seen more than about 3/16" gap (well I have in pictures on the internet ;-) )