John, when cutting out panels I either use the 4-1/2" grinder with a .045 cutoff wheel or a 3" pneumatic cutoff tool with the .035 thick wheel. As an FYI, I normally get mine from the local welding supply, as they carry ones that are made for cutting stainless steel. These do cost a bit more than the cheapies from the flea markets, but last quite a bit longer and you have less of a brown cloud hanging around from cutting wheel particulate floating around.
My cutting method is to fit the new panel the first time, mark with a sharpie, and cut about 3/4" inside that mark (leave extra). Then re-fit the new panel again, as it should fit a little better with the bulk of the old out of the way. Mark it this time with a sharp scribe, cut again leaving about 1/4" extra. Refit one more time, checking the scribe marks for accuracy. If they are off, remark again (may need to use a sharpie to cover the last scribe marks and make the new ones show up better) and trim to the line (leaving the line showing). Refit once more, address any interference areas. You want a nice, tight fit.
This method is more involved, but in many cases you'll find that the initial fit has some interference with adjacent panels, so the first mark is not that accurate. Getting the bulk out of the way will help to insure a more accurate marking for a more accurate fit.
When you are looking at welding in the panel, you want to use consistency with your methods to keep any heat patterns consistent so the shrinking effects are also consistent, making any planishing efforts consistent across the panel as well. If you experience both tight spots and wide gaps in the panel fitment, it will produce larger amounts of heat in the wider gaps as more filler rod (wire feed) is used to "plug the gap" for more shrinkage in those areas, and more puckering and buckles after welding. So looking at the overall job, the more you can do to promote consistency from start to finish, the easier it will be to correct any defects from the welding process.
