Magazines are cheap in comparison to a full auto mini or AC556. If they aren't all factory Ruger 20rnd or 30rnd magazines, then attribute about $12/magazine. Ruger started selling factory 30 round magazines again, so prices have come down substantially. Figure on about $50 - $60 / used factory ruger 30 round mag. Also, the SCAR stock isn't cheap - I've never seen a used one, but I'd bet a used SCAR in excelent condition would sell for $400 or so.
Bottom line - don't worry about the magazines. If you are going to buy a converted Mini-14 make sure that it is at least $1,000 less than the least expensive AC556 you can find. That's just my recomendation. If it's a good conversion, then $4500 or so for the gun itself would be fair. An additional $350 would be fair for the stock.
Also, I'm assuming that you already know your CLEO will sign off on a Form 4. If you don't know this information, make sure you find it out BEFORE you make the deal.