Sooner,
I've installed several heavy varmit M98 mauser barreled actions in Canadian C3 sniper rifle stocks (designed for the Parker-Hale M98 mauser type action), and they ALL had the deep-seated trigger guard/magazine well problem you described.
When I asked my Canadian Forces armorer friend about this, he stated that the C3 sniper stock was intended for heavy field use, and had plenty of stock for sanding and refinishing.
The top of the magazine box on a correctly inletted M98 stock should NOT have hard contact the receiver. If it does, the wood will shrink, and looseness of the magazine box/trigger guard to the receiver will destroy accuracy.
The real purpose of the metal bushing around the rear tang guard screw is to prevent overtightening the rear tang screw which bends the receiver and changes the bedding.
I would inlet the stock to seat the top of the magazine boxl to correct depth but NOT in solid contact with the receiver, and reshape the bottom of the stock to correct the cosmetics.
HTH
John