I know this a tough pill to swallow, but $2500 is not really much to shell out in the bicycle game. Yes, you will probably have to pay for any changes. You bought stock. When you have to change stock parts, you have to pay for new parts. But those stock parts are yours to do with however you please, so don't let them keep them! You can sell them and get some money back (or ask for a credit toward the new parts).

Remember that every bike has a purpose and its geometry reflects that. One may be racier, one may be more relaxed. Sheila has great information on sizing and geometry, so, online, you're getting good advice from her. As for the scratch... no harm in asking about it. Wishing you the best of luck! Fit is paramount for loving your bike. What has the fitter said?