Just my personal opinion....
I would do everything possible to take it back immediately and get the more comfortable Trek instead. All the tweaking in the world will never make a frame with geometry that truly does not suit you into a bike that fits like a glove. I've been there....saddle more forward/more back, shorter handlebars, tilting handlebars, shorter/longer/shorter stem, more core muscle strength, etc etc.....they all improve things but do not totally cure the primary problem...at least for me.
Pay no attention to anyone saying you 'look good' on it. I did that with two knowledgeable bike guys both of whom I totally trusted. I may have looked good (I look good off the bike too! ) but my top tube was still too long by several cm's and my center of gravity wound up being a little too far forward no matter WHAT we did over 2 years to tweak the fit better, and believe me, we did everything. This center of gravity problem is subtle but it has been my own little personal demon. I am keeping this wonderful bike because I am 'mostly' comfortable on it and it's a great bike overall...but I have a new custom bike coming now which I hope will be my 'main' bike and will make me better balanced.

If you can find a bike that feels REALLY comfortable to your body right off the bat, then move Heaven and Earth to get that bike.
I bet that if you tell the Trek LBS to swap out all 105 parts on the Trek to Ultegra, they will be more than happy to accommodate and maybe not even charge you for labor....perhaps just the money difference for the components, if you are fairly assertive and they are feeling cooperative that day.

End of personal opinion.