Your saddle is far to low indicating that the frame is too big for you (do a Google image search for cyclcocross bike to see what it should be). Needing to shorten the stem also indicates sizing issues.

For the 'short cuts' manufactures don't make these, they spec to a price point, if you wanted better spec'd parts, you buy accordingly.

For what to change, would make a list of all the components, and what you would like to change them to, vs buying a bike with them fitted, is it worth it before they have worn out?