You should be fine... Filing the magazines for proper fit is normal... I have an ATI stock, and the mags fit just fine... HOWEVER, the front of the mags were mashing into the receiver, so the firearm was no longer feeding correctly. Upon inspection of the magazines, I noticed an area that was being bitten by the receiver... A short blast with the dremmel on each mag made for a perfect fit, with only 1 jam so far (caused when the round got stuck between the Wartak and the receiver).
After you clean it, and smash some solvent and lube in there you should be 100% ready to rock. The most important thing is to take a look at the bolt, and give'r a good shake. If you here a rattling around, the firing pin is moving freely. If it's not, finger the firing pin from the rear, and if it feels springy and goes back to the full aft position it means he has a spring loaded firing pin installed (safety bonus x10).
Sorry for the innuendos... I can't help myself when it comes to these beautiful little firearms.