Sorry to hear about your bike...Good luck on the painting project! I'm a painting contractor and paint houses for a living...but next week I'm putting the brush down and going to Tmac for the first time!
Becareful and stay on top of that shop. Most places who give answers like that will be happy to take advantage of you, you should describe your symtptoms here so we can give you a hypothetical diagnosis. I'm a mechanic, have worked in several repair shops, and I can tell you first hand, any place that can't diagnose a VFR engine within a few hours isn't qusalified to work on it. Especially engine trouble, our engines are very simple, we have a standard block without pressed cases, so checking internals is as easy as dropping the pan or pulling a valve cover.
Whatever you do, do not accept the "thousands" figure, if you have engine trouble and they don't recommend a used engine which can be had for $500, they are not looking out for your best interest.