Send a link to your local bike shop on this thread regarding the chain line and have them inspect it. Praxis will send a free replacement but they've only had a 32 tooth in stock and stock is 30. I think the 32 is very tight and frankly, if you're looking to get in shape you'll want the 30. If Praxis doesn't have the 30t, look at the cheaper replacements and / or, if the bike store is good, they can probably get you the proper one for zero charge.
Keep an eye on your fork, if it makes the annoying sound that a lot of us our experiencing, tell them Giant has a fix and that should be taken care of.
It is hella annoying to have issues with a $1500 bike but these are relatively minor ones all things considered. Still wish Giant was better at this. This all being said, I now have 500 miles on my 29er Fathom 2 and enjoy the bike. There's not much that can go wrong with it after these fixes and there's something to be said for the reliability / simpleness of a hard tail.