notching the frame
Unless you want to rebuild and completely refabricate the frame kick, thats the safest way to go. Your frame is in all likelyhood C channel. If you notch that you will effectively have only a piece of angle iron over the axle, and that wont have the strength to hold up your body. Eventually what would happen is that the body would start to warp from the frame kick back, and the more weight you put back in the trunk the sooner and worse the warpage would be. To box in the frame, you will want to get a piece of crs, the same thickness as your frame rail, usually about 1/8th inch. Once you have your notch cut, take a piece of carboard and make a template of your frame rail, at least 6 inches to either side of the notch. Cut the CRS, to match your template and weld it in to the open side of your frame rail. Then get a piece of steel tubing of the same diameter or form a strip of the CRS to conform to the notch, and weld it in as well. This will insure the structural integrity of the frame rail. IF your frame is already boxed from the factory, rather than C channel, then all that is needed is to weld in a piece formed to match your notch to replace the part of the lower side of the frame rail that you removed.
The other option would be to weld a piece of boxed steel over the top of where you plan to notch it, then remove that portion of the frame rail. The piece you weld on should pass to at least 6 inches in front of and to the rear of the notch. This may also necessitate cutting holes in your trunk floor to allow the added pieces to be installed. I would also take the piece you place over the top of the frame kick and taper both ends down at a 45 degree angle. Weld the added piece at all points where it touches the frame rail. I would also weld in a piece up into the notch to cover the ends of the frame rail left from the cut.
Welding the box tubing piece over the top then notching the frame will give you the additional clearance of the thickness of the frame rail.