1. I'm packing my merino tshirt (x2, one for sleeping), long sleeve and hoody (also both merino), I also have hiking pants and 2x thermals (also one for sleeping) for the bottom half. Not enough or over kill?
What will you wear out to dinner in the evenings if your one pair of hiking pants is wet? Maybe your second "thermals" could be used for that (depending on your personal fashion statement , or you replace one pair with a dual purpose pant.
2. I have a poncho for rain and am considering gaiters but am also considering the hard shell and rain pants + rain cover combination. Thoughts on this?
My thoughts are that I prefer rain jacket and pants, but others prefer ponchos.
3. I have great waterproof hiking shoes and will be wearing merino socks (but also have synthetic too). Also with rain pants/gaiters do you think they will be ok with all the mud?
They will be as OK as anything, and better than many footwear choices! In other words, if the mud is bad you cannot avoid a mess.