A custom is never worth in $$ what you put in it, but if it's what you want, no reason not to go for it. Just think long and hard and ask yourself can you afford to take a big loss on the resale price if it turns out less cool when you've paid for it than you expected it to be.
Suggestion on the gunsmith: find another gunsmith. Long gun shipping is usually $20 each way, and there are a lot of gunsmiths in the country. Probably some of them specialize in the Mini-Mauser. You might ask in the gunsmithing forum over on Accurate Reloading (as always, use the search first), since several memebers there have played with the Mini Mauser action. Opening a bolt face is done all the time. While there could be some special gotchas with the Mini-Mauser, it sounds more likely it's just work your gunsmith doesn't want or isn't experienced in. Altering the magazine might or might not be a bigger problem.
Suggestion on the action: if the price is favorable and affordable, and if you ever expecct to build a custom on a .223-length action, buy it regardless of whether or not you plan to use it now. There aren't too many small left-hand actions out there for less than princely sums, and Remington shows no interest in importing any more of the left-hand Mini-Mausers (or any bare actions either, from what I read).