I agree with others as to the drawbacks to going 9 speed and also doing a short term piecemeal approach ... unless you really find bargain parts and like doing the work yourself.

By your complaint about the tuneup, I have to assume you don't do your own mechanical work. Therefore, my opinion is that you should just buy a bike of the level you want and can afford.

That said, there is NO REASON the sora group shouldn't work pretty darn good. As good as 105/Ultegra/Dura Ace? maybe not, but it should shifd cleanly and accurately. Every Sora bike I've ever used (they are common on rentals), as well as my daughter's Sora bike work pretty much perfectly.

Id get to the bottom of the problem, either learning to do it yourself, making the LBS do it right, or finding a new LBS. Save your money and buy a new bike with better components all around if that's the way you think you should go in the long run.