I talked to Larry at APE and to Merrit Carden. Both were exceptionally nice and helpful. Both were of the definite opinion that a freshly rebuild tranny should NOT grind in first.
Larry and Merrit both are very smart and experienced guys, but they're essentially wrong on this one. With the design of the Alfa transmission, the first gear synchronizer DOES NOT ENGAGE at all going from neutral to first. There is a piece in the other gears that is not in the first gear assembly. Maybe with brand new, sharp, dog teeth on first it might be better, but the underlying problem will always be there.
Now, Robert's modification will fix this issue, but it's not widely known and unless you discussed making this change before the rebuild it would not be considered a "standard" part of the job. So I don't think the fact that it still does this should be considered a mistake by the mechanic. On the first gear grinding, suggest you either:
1) Do what most Alfa guys do and touch another gear before shifting into first, or:
2) Have the mechanic add the parts per Robert's instructions, but pay for the labor/parts on this as an extra item
The poor shifting, on the other hand, sounds like a real issue. If I were you, I would focus on having him fix the "clonk" since that isn't good. Did he ever test drive the car? What did he say about the issues you reported?