It's good you read through everything here trying to work it out, but the fundamental place you've gone wrong is in using automap. You don't want automap at all for this, you just want bog standard midi mapping.
To this end, you should use a template in the Novation that is not automap-related, but above all, you should completely turn off the automap software on your computer. If you turn it off or delete it, there's no way it can activate. I mean it's been 9 months since I did my initial setup, but I recall that I just made a zipped archive of the automap software application, and kept that handy in case I ever did want it, but then I deleted the automap app itself. This stopped it from ever turning on. There may be a less drastic way that I've forgotten, but it's not a big deal.
Once you've done that, the relationship between Live and the Novation should just be 1-way. You send messages out of the Novation, through its virtual port 1, and they are received by Live. So you're right to stick with port 1 in Live's preferences, and DON'T set it so that Live is going anyway in the 'out' tabs.
With this 1-way flow, the Novation can't make decisions for you. You don't want it changing templates based on what it thinks is right by polling your computer. You want it to stick with the template you've chosen and are working on.
Summary version of this is -- turn the dial on the Novation to select the template you're going to use and work on. Then press 'global' - then press 'write' twice... I'm going on memory here, but this will set the current template to be the one that boots when the Novation is turned on. Then press 'play' again.
This is a bit crash coursey, but I'm trying to just get you on the right track. For details on performing specific actions mentioned here, the Novation manual should be able to help.