I think you should return the boots. In a few weeks (hopefully) they will feel out of season as the weather warms up, so best waiting until A/W stuff comes in again before buying boots. Get some spring footwear instead. Either some converse, or some ballet flats, both will go well with skinnies but can give a very different look.
It almost sounds like you are trying to talk yourself out of keeping the boots - the main positive is how flat they are, but you can find other flat footwear that is more suitable.
I can't get the jacket link to work either, but it sounds nice, and on trend. The layered look is not an issue and can actually add interest to a plainer outfit. I'd consider getting a nice scarf too to finish off the look.
As for the coat, I think it is just ok. But as with the boots, we are getting into spring time now, so you are probably best waiting until autumn to get your next winter coat.
So my verdict is return the boots and coat.