The problem with "stopping dead" isn't just this engine. My PS3 RK Imperial Mikado does it as well when operating under conventional control. Under DCS, it coasts gently to a stop. I've opened a dialog with MTH regarding the problem and will report back anything that I learn.
The issue with bottoming out the rollers on the screw heads when traveling the GraGraves uncouplers isn't all that surprising. MTH, like all of the manufacturers who also sell track, design their engines to work optimally with their track. These manufacturers may not and, frankly, shouldn't have to ensure that their products work well with their competitors' products.
I regularly find that my smaller MTH steamers often have issues with my 6-turnout Ross switch ladder. I have a variety of ways to remedy the problem so that these engines can crawl over the turnout ladder at 2 SMPH. Thus far, I haven't found any that I couldn't modify slightly (and non-invasively) to correct any such problems.
As far as the pulling power of the engine, I haven't seen too many issues like the one that you describe. I tend to operate relatively short trains (6-10 cars), however, I have one really wretched grade that is excessively steep and has an O42 quarter-curve in the middle. Some engines can be challenged a bit moving from the layout's middle level to its upper level.
