If as you say he didn't mention or show any photos of the repairs to the bracket(s) or lever(s), that probably gives you some standing to complain. Doing so won't cost you anything except a little time. At $300, it was I think less than average going price. Apparently there's nothing wrong with the main casting. If you don't have to replace any of the gears, you can probably rebuild it without exceeding the average. At least if you don't count the labor. It depends on what you have to do to the shafts. And assumes you don't have to replace any gears.
If you turn down the ends of the shafts and use under size bushings, you will also need to bush the collars I think. I would get price and availability on new shafts and also get a local machine shop to quote you prices. I don't much like the idea of turning down the existing shafts.
If you don't buy the replacement bushings from Clausing (which I would probably do), I think that I would use Oilite bushings. However, if you do that and if you have to bore any of them, you should hold the bushings in collets and use a sharp single-point boring bar, not a reamer.