I have an early WASR that has the welded on nut, and yours sound just like mine by your descrption. I never bothered to remove it, as Ive heard that some have no threads under the nut at all. My WASR's sights where nice and straight, and it also came without a hint of trigger slap, unlike my SAR.
My SAR's front sight has a slight cant, but it doenst affect accuracy, and both it and the WASR are very good shooters, and on par with other AKs I have that cost twice the money or more. The SAR has no threads at the muzzle.
You can remove the nut and add a brake or flash suppressor with out issue now. Ive done it on a couple of AK's, as well as a couple of AR's that were of the "ban" era. The AK's were just crappy welds (not like the WASR's weld though), and came off pretty easily, the AR's on the other hand, were blind pinned and welded, and a good deal more work. I suppose the only thing thing that may be an issue, is what your state laws are, or if the barrel is shorter than 16", and the muzzle device on there is permanently attached to make it legal. Not an issue in your case, but it can be with some guns. My Krebs AK103K is an example there. It has a 14" barrel with a permanently attached brake.
The magazine issue is a common one, and all my AK's have it at some point, depending on the mag in the gun. One mag will wobble in one gun, and not in another, and the "dimples" arent the issue. I guess its just what it is. Its never been a problem with reliability, and wobble or not, the guns shoot just fine.